NAR Web Server Issue (July 1, 2009)
Source: http://nar.oxfordjournals.org/content/vol37/suppl_2/index.dtl
Total Links: 113
3D-DART
DNA >
Structure and Sequence Feature Detection
The 3D-DART web server interfaces to a collection of tools for the generation of DNA structural models in custom conformations.
The 3D-DART web server interfaces to a collection of tools for the generation of DNA structural models in custom conformations.
@TOME-2
Protein >
3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization
@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization
@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.
ANNIE
Protein >
Annotation and Function
ANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer.
ANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer.
ATIVS
Model Organisms >
Microbes
Sequence Comparison > Comparative Genomics
ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.
Sequence Comparison > Comparative Genomics
ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.
AutoClass@IJM
Expression >
Gene Set Analysis
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
Human Genome > Genomics
Protein > Protein Expression
AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
Human Genome > Genomics
Protein > Protein Expression
AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.
BioBIKE
Computer Related >
Web Services
BioBIKE is a web-based environment enabling biologists with little programming expertise to combine tools, data and knowledge in novel and complex ways. BioBIKE is composed of three components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Users may also invent their own tools.
BioBIKE is a web-based environment enabling biologists with little programming expertise to combine tools, data and knowledge in novel and complex ways. BioBIKE is composed of three components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Users may also invent their own tools.
BioMart
DNA >
Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).
BioPortal
DNA >
Annotations
Expression > Transcript Expression & Microarrays
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools
BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.
Expression > Transcript Expression & Microarrays
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools
BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.
CentroidFold
RNA >
Structure Prediction, Visualization, and Design
Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).
Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).
ClanTox
Sequence Comparison >
Analysis of Aligned Sequences
ClanTox, a classifier of short animal toxins, predicts whether input sequences are toxin-like based on classification system training to known animal toxins. This dscovery prediction tool also outputs presence of signal peptide, the number of cysteine residues and the associated functional annotations.
ClanTox, a classifier of short animal toxins, predicts whether input sequences are toxin-like based on classification system training to known animal toxins. This dscovery prediction tool also outputs presence of signal peptide, the number of cysteine residues and the associated functional annotations.
COFECO
DNA >
Annotations
Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes
COFECO is a web-based tool for composite annotation of protein complexes, KEGG pathways and Gene Ontology terms for an input class of genes. COFECO provides a GO hierarchical viewer and KEGG pathway viewer for visualizing enrichment results.
Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes
COFECO is a web-based tool for composite annotation of protein complexes, KEGG pathways and Gene Ontology terms for an input class of genes. COFECO provides a GO hierarchical viewer and KEGG pathway viewer for visualizing enrichment results.
COMPASS
Sequence Comparison >
Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching
COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.
Sequence Comparison > Similarity Searching
COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.
COPS
Protein >
3-D Structure Comparison
Protein > 3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.
Protein > 3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.
CVTree
Model Organisms >
Microbes
Protein > Phylogeny Reconstruction
Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.
Protein > Phylogeny Reconstruction
Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.
d-Omix
Protein >
Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.
DASMIweb
Protein >
Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
The DASMIweb server allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.
Protein > Sequence Retrieval
The DASMIweb server allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.
DIANA-microT
Expression >
Gene Regulation
Human Genome > Genomics
RNA > Functional RNAs
The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources.
Human Genome > Genomics
RNA > Functional RNAs
The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources.
EBI Tools
Computer Related >
Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching
EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.
FASTR3D
Protein >
3-D Structure Comparison
RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Pairwise Sequence Alignments
FASTR3D is a web based search tool that allows users to search the PDB database for structurally similar RNAs from input queries of PDB coordinates for an RNA molecule, an RNA secondary structure or RNA primary sequence.
RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Pairwise Sequence Alignments
FASTR3D is a web based search tool that allows users to search the PDB database for structurally similar RNAs from input queries of PDB coordinates for an RNA molecule, an RNA secondary structure or RNA primary sequence.
FMM
Other Molecules >
Metabolites
Protein > Interactions, Pathways, Enzymes
From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.
Protein > Interactions, Pathways, Enzymes
From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.
G-SESAME
Expression >
Gene Set Analysis
Literature > Text Mining
Sequence Comparison > Comparative Genomics
G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.
Literature > Text Mining
Sequence Comparison > Comparative Genomics
G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.
Gendoo
DNA >
Annotations
Expression > Gene Set Analysis
Human Genome > Genomics
Literature > Text Mining
Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.
Expression > Gene Set Analysis
Human Genome > Genomics
Literature > Text Mining
Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.
GeneCodis
Computer Related >
Web Services
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks
Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks
Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.
GeneSet2miRNA
Expression >
Gene Regulation
Expression > Gene Set Analysis
GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.
Expression > Gene Set Analysis
GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.
GeNMR
Protein >
3-D Structure Prediction
Generate NMR structures (GeNMR) is a web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.
Generate NMR structures (GeNMR) is a web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.
GenoCAD
DNA >
Tools For the Bench
Expression > Networks
Expression > Protein Expression
GenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.
Expression > Networks
Expression > Protein Expression
GenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.
GeSBAP
Expression >
Gene Set Analysis
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.
GoGene
DNA >
Annotations
Literature > Text Mining
GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.
Literature > Text Mining
GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.
HHomp
DNA >
Gene Prediction
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
HHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
HHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.
HMS-ICS
Computer Related >
Databases
The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the conversion of data IDs using the corresponding tables in HMS.
The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the conversion of data IDs using the corresponding tables in HMS.
HomozygosityMapper
DNA >
Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
A web base approach to homozygosity mapping. Users upload SNP genotype files into a marker database for analysis and detection of long homozygous stretches.
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
A web base approach to homozygosity mapping. Users upload SNP genotype files into a marker database for analysis and detection of long homozygous stretches.
HorA
Protein >
3-D Structure Comparison
Sequence Comparison > Similarity Searching
HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures.
Sequence Comparison > Similarity Searching
HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures.
HotSpot Wizard
Protein >
Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features
HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features
HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.
IC50-to-Ki
Other Molecules >
Compounds
Other Molecules > Small Molecules
Protein > Biochemical Features
A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.
Other Molecules > Small Molecules
Protein > Biochemical Features
A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.
iCODEHOP
DNA >
Tools For the Bench
iCODEHOP is an interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers for multiple alignment of protein sequences.
iCODEHOP is an interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers for multiple alignment of protein sequences.
Insignia
Model Organisms >
Microbes
Insignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.
Insignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.
INTREPID
Protein >
Annotation and Function
Protein > Sequence Features
The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.
Protein > Sequence Features
The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.
iSARST
Protein >
3-D Structure Comparison
Protein > 3-D Structure Retrieval, Viewing
Protein > Proteomics
iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.
Protein > 3-D Structure Retrieval, Viewing
Protein > Proteomics
iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.
jpHMM
Model Organisms >
Microbes
Model Organisms > Other Organisms
Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.
Model Organisms > Other Organisms
Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.
LitInspector
Literature >
Text Mining
Protein > Interactions, Pathways, Enzymes
A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.
Protein > Interactions, Pathways, Enzymes
A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.
MaXIC-Q
Protein >
Proteomics
The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.
The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.
MedlineRanker
Literature >
Text Mining
The MedlineRanker web server allows a flexible ranking of Medline for a topic of interest without expert knowledge.
The MedlineRanker web server allows a flexible ranking of Medline for a topic of interest without expert knowledge.
MEME Suite
DNA >
Structure and Sequence Feature Detection
Sequence Comparison > Comparative Genomics
The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms.
Sequence Comparison > Comparative Genomics
The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms.
MEME Suite
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics
The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics
The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.
MetaboAnalyst
Other Molecules >
Metabolites
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics
MetaboAnalyst is a web server for metabolic data analysis. Users input a choice of data (NMR peaks, binned spectra, MS peaks, etc) for data processing, normalization, multivariate statistical analysis, graphing, metabolite identification and pathway mapping.
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics
MetaboAnalyst is a web server for metabolic data analysis. Users input a choice of data (NMR peaks, binned spectra, MS peaks, etc) for data processing, normalization, multivariate statistical analysis, graphing, metabolite identification and pathway mapping.
mGene.web
DNA >
Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources
mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.
Human Genome > Genomics
Model Organisms > General Resources
mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.
MGIP
DNA >
Mapping and Assembly
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Pairwise Sequence Alignments
The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Pairwise Sequence Alignments
The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.
Microbe Browser
Model Organisms >
Microbes
The Microbe Browser is a web server providing comparative microbial genomics data integrated from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) databases. Gene predictions based on 5 software packages is also displayed.
The Microbe Browser is a web server providing comparative microbial genomics data integrated from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) databases. Gene predictions based on 5 software packages is also displayed.
miRanalyzer
Expression >
Gene Regulation
Human Genome > Genomics
RNA > Functional RNAs
miRabakyzer is a web server tool for the analysis of deep sequencing experiments for small RNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs.
Human Genome > Genomics
RNA > Functional RNAs
miRabakyzer is a web server tool for the analysis of deep sequencing experiments for small RNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs.
MirZ
Expression >
cDNA, EST, SAGE
Expression > Gene Regulation
RNA > Functional RNAs
MirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.
Expression > Gene Regulation
RNA > Functional RNAs
MirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.
MMIA
Expression >
Gene Regulation
Expression > Transcript Expression & Microarrays
Human Genome > Genomics
RNA > Functional RNAs
microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).
Expression > Transcript Expression & Microarrays
Human Genome > Genomics
RNA > Functional RNAs
microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).
MolLoc
Protein >
3-D Structural Features
Protein > 3-D Structure Comparison
Molecular Local surface comparison (MolLoc) is a web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues.
Protein > 3-D Structure Comparison
Molecular Local surface comparison (MolLoc) is a web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues.
NetCSSP
Protein >
2-D Structure Prediction
A web application based on contact-dependent secondary structure propensity calculations for predicting chameleon sub-sequences that may contribute to amyloid fibril formation. NetCSSP also contains precalculated non-native secondary structure propensities for 1.4 million fragments of 7 residue length from PDB structures.
A web application based on contact-dependent secondary structure propensity calculations for predicting chameleon sub-sequences that may contribute to amyloid fibril formation. NetCSSP also contains precalculated non-native secondary structure propensities for 1.4 million fragments of 7 residue length from PDB structures.
NNcon
Protein >
3-D Structural Features
Protein > 3-D Structure Prediction
Using 2D-recursive neural networks, NNcon is a web server for predicting protein contact maps.
Protein > 3-D Structure Prediction
Using 2D-recursive neural networks, NNcon is a web server for predicting protein contact maps.
OmicBrowse
DNA >
Utilities
OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. Multiple users may access a common dataset.
OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. Multiple users may access a common dataset.
OptiTope
Human Genome >
Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Molecular Dynamics and Docking
OpiTope identifies the optimal set of peptides or epitopes for a vaccine given constraints such as MHC allele probabilities, peptide mutation rates and maximum number of selected peptides. Incorporated as part of the EpiToolKit.
Human Genome > Sequence Polymorphisms
Protein > Molecular Dynamics and Docking
OpiTope identifies the optimal set of peptides or epitopes for a vaccine given constraints such as MHC allele probabilities, peptide mutation rates and maximum number of selected peptides. Incorporated as part of the EpiToolKit.
Orphelia
DNA >
Gene Prediction
Orphelia is a machine learning program for predicting genes in short DNA sequences from metagenomic sequencing projects. The program encompasses fragment length specific prediction models for chain termination sequencing and pyrosequencing.
Orphelia is a machine learning program for predicting genes in short DNA sequences from metagenomic sequencing projects. The program encompasses fragment length specific prediction models for chain termination sequencing and pyrosequencing.
OrthoSelect
DNA >
Phylogeny Reconstruction
Expression > cDNA, EST, SAGE
Sequence Comparison > Pairwise Sequence Alignments
OrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.
Expression > cDNA, EST, SAGE
Sequence Comparison > Pairwise Sequence Alignments
OrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.
PathExpress
Expression >
Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.
Protein > Interactions, Pathways, Enzymes
PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.
PEP-FOLD
Protein >
3-D Structure Prediction
PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution.
PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution.
PHEMTO
Protein >
3-D Structural Features
Protein > Biochemical Features
Protein pH-dependent Electric Moment Tools (PHEMTO) is a web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format; output is electric/dipole moments and interactive visualization as well as the full electrostatic characteristics.
Protein > Biochemical Features
Protein pH-dependent Electric Moment Tools (PHEMTO) is a web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format; output is electric/dipole moments and interactive visualization as well as the full electrostatic characteristics.
PHOG
Protein >
Phylogeny Reconstruction
The PHOG web server identifies orthologs based on precomputed phylogenetic trees in the PhyloFacts resource. Users may target different taxonomic distances and precision levels by using tree-distance thresholds.
The PHOG web server identifies orthologs based on precomputed phylogenetic trees in the PhyloFacts resource. Users may target different taxonomic distances and precision levels by using tree-distance thresholds.
PhyloPars
Protein >
Phylogeny Reconstruction
The PhyloPars web server allows for easy, efficient estimation of metabolic parameters as inferred from observations on species that are phylogenetically related.
The PhyloPars web server allows for easy, efficient estimation of metabolic parameters as inferred from observations on species that are phylogenetically related.
PLAN2L
Literature >
Text Mining
Model Organisms > Plants
A web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana.
Model Organisms > Plants
A web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana.
PLecDom
DNA >
Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments
PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments
PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.
Pomelo II
Expression >
Protein Expression
Expression > Transcript Expression & Microarrays
Pomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc.
Expression > Transcript Expression & Microarrays
Pomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc.
PosMed
Human Genome >
Health and Disease
Literature > Text Mining
Model Organisms > Mouse and Rat
Model Organisms > Plants
To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based on direct and indirect inference of the hit documents. PosMed currently supports prioritization of positional cloning candidate genes in human, mouse, rat and Arabidopsis thaliana.
Literature > Text Mining
Model Organisms > Mouse and Rat
Model Organisms > Plants
To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based on direct and indirect inference of the hit documents. PosMed currently supports prioritization of positional cloning candidate genes in human, mouse, rat and Arabidopsis thaliana.
PPISearch
Protein >
Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Similarity Searching
PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Similarity Searching
PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.
PREP Suite
Model Organisms >
Plants
RNA > Motifs
The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.
RNA > Motifs
The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.
primers4clades
DNA >
Tools For the Bench
Protein > Phylogeny Reconstruction
Primers4clades is a web server that uses phylogenetic trees to design primers to amplify novel sequences from across species using metagenomic DNA or from uncharacterized organisms. Beginning with a set of non-aligned protein coding genes, primers4clades aligns the sequences, computes a neighbor-joining tree and designs lineage specific primers for the user selected species or sequence clusters.
Protein > Phylogeny Reconstruction
Primers4clades is a web server that uses phylogenetic trees to design primers to amplify novel sequences from across species using metagenomic DNA or from uncharacterized organisms. Beginning with a set of non-aligned protein coding genes, primers4clades aligns the sequences, computes a neighbor-joining tree and designs lineage specific primers for the user selected species or sequence clusters.
ProGMap
Protein >
Annotation and Function
Protein > Proteomics
Protein > Sequence Comparison
Protein Group Mappings (ProGMap) facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences mapped to 240,000 protein groups. Queries through ProGMap may be made using sequence identifiers, gene symbols, protein functions or amino acid sequences.
Protein > Proteomics
Protein > Sequence Comparison
Protein Group Mappings (ProGMap) facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences mapped to 240,000 protein groups. Queries through ProGMap may be made using sequence identifiers, gene symbols, protein functions or amino acid sequences.
ProSMoS
Protein >
2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern.
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern.
ProteDNA
Protein >
Domains and Motifs
Protein > Sequence Features
ProteDNA identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction.
Protein > Sequence Features
ProteDNA identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction.
ProteinCCD
DNA >
Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval
Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval
Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.
Protinfo PPC
Protein >
Interactions, Pathways, Enzymes
Protinfo Prediction of Protein Complex (PPC) is a web server that predicts atomic level structures of interacting proteins from their amino acid sequences.
Protinfo Prediction of Protein Complex (PPC) is a web server that predicts atomic level structures of interacting proteins from their amino acid sequences.
Pscan
Expression >
Gene Regulation
Expression > Gene Set Analysis
Expression > Transcript Expression & Microarrays
Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.
Expression > Gene Set Analysis
Expression > Transcript Expression & Microarrays
Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.
PubChem BioAssay Service
Other Molecules >
Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking
PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking
PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.
QMEAN
Protein >
3-D Structure Prediction
QMEAN is a web server for protein model quality estimation. Either the composite scoring function QMEAN or the clustering based scoring function QMEANclust may be used.
QMEAN is a web server for protein model quality estimation. Either the composite scoring function QMEAN or the clustering based scoring function QMEANclust may be used.
RASMOT-3D PRO
Protein >
3-D Structural Features
The RASMOT-3D PRO web server performs systematic searches in 3D protein structures for a set of residues exhibiting a particular topology. Input is a PDB file for the motif of interest; output is an interactive list of protein structures exhibiting resides of similar topology.
The RASMOT-3D PRO web server performs systematic searches in 3D protein structures for a set of residues exhibiting a particular topology. Input is a PDB file for the motif of interest; output is an interactive list of protein structures exhibiting resides of similar topology.
RegAnalyst
DNA >
Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
RegAnalyst is a web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database).
Expression > Gene Regulation
Model Organisms > Microbes
RegAnalyst is a web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database).
RHYTHM
Protein >
3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact type and conservation of each residue.
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact type and conservation of each residue.
RNAmutants
RNA >
Structure Prediction, Visualization, and Design
A web server to explore the effect of mutations on the RNA secondary structures.
A web server to explore the effect of mutations on the RNA secondary structures.
RosettaAntibody
Protein >
3-D Structure Prediction
The RosettaAntibody server predicts the structure of an antibody variable region given the amino acid sequences of the light and heavy chains. 2000 independent structures are generated and scored, with the top 10 models being returned in high resolution and detailed format.
The RosettaAntibody server predicts the structure of an antibody variable region given the amino acid sequences of the light and heavy chains. 2000 independent structures are generated and scored, with the top 10 models being returned in high resolution and detailed format.
SALAMI
Protein >
3-D Structure Comparison
Protein > 3-D Structure Retrieval, Viewing
The SALAMI web server searches the protein data bank (PDB) for structures similar to input coordinates of a protein chain. Output is provided in a simple structure viewer with details of the sequence, structural similarity and sequence alignments.
Protein > 3-D Structure Retrieval, Viewing
The SALAMI web server searches the protein data bank (PDB) for structures similar to input coordinates of a protein chain. Output is provided in a simple structure viewer with details of the sequence, structural similarity and sequence alignments.
SAM-T08
Protein >
2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Sequence Features
The SAM-T08 web server is a 3D protein structure prediction server. The server also provides 3 multiple sequence alignments of putative homologs, prediction of local structural features including backbone and burial properties and residue-residue contact predictions.
Protein > 3-D Structure Prediction
Protein > Sequence Features
The SAM-T08 web server is a 3D protein structure prediction server. The server also provides 3 multiple sequence alignments of putative homologs, prediction of local structural features including backbone and burial properties and residue-residue contact predictions.
SARA
Protein >
3-D Structure Comparison
RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design
Based on the SARA program, the SARA server computes pairwise alignment of RNA structures for structure based assignment of RNA function.
RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design
Based on the SARA program, the SARA server computes pairwise alignment of RNA structures for structure based assignment of RNA function.
seeMotif
Protein >
3-D Structural Features
Protein > 3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
The web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).
Protein > 3-D Structure Retrieval, Viewing
Protein > Domains and Motifs
The web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).
SENT
Literature >
Text Mining
SENT is a text mining web server. SENT uses non-negative matrix factorization to identify topics in scientific articles associated with an input list of genes.
SENT is a text mining web server. SENT uses non-negative matrix factorization to identify topics in scientific articles associated with an input list of genes.
SEPPA
Protein >
3-D Structure Prediction
A computational server for Spatial Epitope Prediction of Protein Antigens (SEPPA) based on a 'unit patch of residue triangle' description of local spatial context in protein surface.
A computational server for Spatial Epitope Prediction of Protein Antigens (SEPPA) based on a 'unit patch of residue triangle' description of local spatial context in protein surface.
SePreSA
Other Molecules >
Compounds
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking
SePreSA is a server for the prediction of populations susceptible to serious adverse drug reactions. A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program.
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking
SePreSA is a server for the prediction of populations susceptible to serious adverse drug reactions. A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program.
SIB-BLAST
Sequence Comparison >
Pairwise Sequence Alignments
SIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection.
SIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection.
SITEHOUND-web
Protein >
3-D Structural Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking
SITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (i.e. carbon probe, phosphate probe) and displays the putative sites in interactive 3D representation.
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking
SITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (i.e. carbon probe, phosphate probe) and displays the putative sites in interactive 3D representation.
SLITHER
Protein >
3-D Structural Features
Protein > Biochemical Features
Protein > Molecular Dynamics and Docking
SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.
Protein > Biochemical Features
Protein > Molecular Dynamics and Docking
SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.
SNOW
Protein >
Interactions, Pathways, Enzymes
SNOW is a web-based tool for the statistical analysis of protein-protein interaction networks. Input is a collection of protein or gene indentifiers onto the interactome scaffold. Output includes statistical significance estimates.
SNOW is a web-based tool for the statistical analysis of protein-protein interaction networks. Input is a collection of protein or gene indentifiers onto the interactome scaffold. Output includes statistical significance estimates.
SNPinfo
DNA >
Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs
A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs
A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.
SplitPocket
Protein >
3-D Structural Features
Protein > Molecular Dynamics and Docking
SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >26,000 structures in PDB have been found to have split pockets.
Protein > Molecular Dynamics and Docking
SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >26,000 structures in PDB have been found to have split pockets.
SROOGLE
Expression >
Splicing
SROOGLE is a webserver that makes splicing signal sequence and scoring data available to the biologist in an integrated, visual and user friendly format.
SROOGLE is a webserver that makes splicing signal sequence and scoring data available to the biologist in an integrated, visual and user friendly format.
SuperLooper
Protein >
3-D Structural Features
SuperLooper is a web tool for the modeling of loops in globular and membrane proteins.
SuperLooper is a web tool for the modeling of loops in globular and membrane proteins.
TmPrime
DNA >
Mapping and Assembly
DNA > Tools For the Bench
TmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression.
DNA > Tools For the Bench
TmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression.
TOPCONS
Protein >
2-D Structure Prediction
Protein > Sequence Comparison
Sequence Comparison > Pairwise Sequence Alignments
TOPCONS is a web server for consensus prediction of membrane protein topology. Users may constrain parts of the input protein sequence to known inside/outside location.
Protein > Sequence Comparison
Sequence Comparison > Pairwise Sequence Alignments
TOPCONS is a web server for consensus prediction of membrane protein topology. Users may constrain parts of the input protein sequence to known inside/outside location.
ToppGene Suite
Expression >
Gene Set Analysis
Expression > Networks
ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.
Expression > Networks
ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.
Torque
Protein >
Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Torque is a web server for querying of protein-protein interaction networks or pathways across species. Networks of up to 25 proteins may be input.
Protein > Phylogeny Reconstruction
Torque is a web server for querying of protein-protein interaction networks or pathways across species. Networks of up to 25 proteins may be input.
UniPrime2
DNA >
Tools For the Bench
The UniPrime2 web server designs large sets of universal primers when provided with a gene reference ID or FASTA sequence. UniPrime2 works by integrating Blastn, T-Coffee, GramAlign and Primer3 into a single software pipeline.
The UniPrime2 web server designs large sets of universal primers when provided with a gene reference ID or FASTA sequence. UniPrime2 works by integrating Blastn, T-Coffee, GramAlign and Primer3 into a single software pipeline.
Virus Genotyping Tools
DNA >
Phylogeny Reconstruction
Model Organisms > Microbes
This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.
Model Organisms > Microbes
This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.
VisANT
Expression >
Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
Protein > Interactions, Pathways, Enzymes
VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.
VisANT 3.5
Expression >
Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
VisANT is an integrative software platform for the visualizing, mining, analysis and modeling of biological networks. New functions in VisANT allow determination of over-representation and expression enrichment.
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression & Microarrays
VisANT is an integrative software platform for the visualizing, mining, analysis and modeling of biological networks. New functions in VisANT allow determination of over-representation and expression enrichment.
VisHiC
Expression >
Gene Set Analysis
Expression > Transcript Expression & Microarrays
VisHiC is a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.
Expression > Transcript Expression & Microarrays
VisHiC is a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.
Web 3DNA
DNA >
Structure and Sequence Feature Detection
The web 3DNA server is the web interface for the 3DNA suite of programs developed for the analysis, reconstruction and visualization of 3D nucleic acid containing structures.
The web 3DNA server is the web interface for the 3DNA suite of programs developed for the analysis, reconstruction and visualization of 3D nucleic acid containing structures.
WebGMAP
Expression >
cDNA, EST, SAGE
Human Genome > Genomics
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Pairwise Sequence Alignments
A web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detection and alignment. Users can also sort, filter and search for individual cDNA sequences or alignments.
Human Genome > Genomics
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Pairwise Sequence Alignments
A web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detection and alignment. Users can also sort, filter and search for individual cDNA sequences or alignments.
WebLab
Computer Related >
Web Services
An integrative knowledge sharing system that supports collaboration of biological researchers from various fields. WebLab allows users to fetch, analyze with more than 260 integrated bioinformatic tools, manipulate and share data under an intuitive web interface. These tools can be further organized as customized workflows.
An integrative knowledge sharing system that supports collaboration of biological researchers from various fields. WebLab allows users to fetch, analyze with more than 260 integrated bioinformatic tools, manipulate and share data under an intuitive web interface. These tools can be further organized as customized workflows.
webPRC
Protein >
Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
Web Profile Comparer (webPRC) is a web server for searching for distant homologs or similar alignment in domain databases. Results may be provided as either multiple sequence alignments or aligned hidden Markov models. An alignment editor allows for user editing of output alignments.
Sequence Comparison > Multiple Sequence Alignments
Web Profile Comparer (webPRC) is a web server for searching for distant homologs or similar alignment in domain databases. Results may be provided as either multiple sequence alignments or aligned hidden Markov models. An alignment editor allows for user editing of output alignments.
WhichGenes
Expression >
Gene Set Analysis
WhichGenes is a web based tool for gathering, building, storing and exporting gene sets with application to gene set enrichment analysis. The user may export a gene set in any desired output format with multiple gene identifiers.
WhichGenes is a web based tool for gathering, building, storing and exporting gene sets with application to gene set enrichment analysis. The user may export a gene set in any desired output format with multiple gene identifiers.
wwLigCSRre
Other Molecules >
Compounds
Other Molecules > Small Molecules
Protein > 3-D Structure Comparison
The wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. Inputted 3D ligand molecules may be screened against banks such as Kinase-, CNS-, GPCR-, ion-channel-, antibacterial-, anticancer-, and analgesic-focused libraries or DrugBank database.
Other Molecules > Small Molecules
Protein > 3-D Structure Comparison
The wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. Inputted 3D ligand molecules may be screened against banks such as Kinase-, CNS-, GPCR-, ion-channel-, antibacterial-, anticancer-, and analgesic-focused libraries or DrugBank database.
