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NAR Web Server Issue 2011

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Found 92 links

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firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php [open in a new window]

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Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

links directory index: 128
TitlePublication YearGoogle Scholar Citation Count
firestar--advances in the prediction of functionally important residues20112
FireDB--a database of functionally important residues from proteins of known structure200730
firestar--prediction of functionally important residues using structural templates and alignment reliability200744
SQUARE--determining reliable regions in sequence alignments200452
NAR Web Server Issue 2007NAR Web Server Issue 2011
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g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/ [open in a new window]

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DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

links directory index: 120
TitlePublication YearGoogle Scholar Citation Count
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments2007120
NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

GCViewTool Content

http://toolkit.tuebingen.mpg.de/gcview [open in a new window]

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Protein > Annotation and Function

GCView facilitates the analysis of the genomic context of a query protein. It uses protein homology to assign corresponding genomic context.

This content is being maintained by iwan.grin and AG Linke.

links directory index: 83
TitlePublication YearGoogle Scholar Citation Count
GCView: the genomic context viewer for protein homology searches20112
The MPI Bioinformatics Toolkit for protein sequence analysis200681
NAR Web Server Issue 2011
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tagsamino acid sequence homology computational biology genomic context genomics operon structure protein conformation protein sequence analysis proteins sequence alignment

Gene3DTool Content

http://gene3d.biochem.ucl.ac.uk/WebServices/ [open in a new window]

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Computer Related > Web Services
Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.

This content is being maintained by corinyeats.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences20113
NAR Web Server Issue 2011
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tagshuman genome humans molecular sequence annotation protein databases protein sequence analysis tertiary protein structure

GénieTool Content

http://cbdm.mdc-berlin.de/tools/genie/ [open in a new window]

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Literature > Text Mining and Semantics

Genie evaluates the literature attached to all genes in a genome and to their orthologs for a selected topic. Hundreds of species and millions of genes are supported. Running times range from a few seconds to a minute in most of the cases.

This content is being maintained by fontaine.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Génie: literature-based gene prioritization at multi genomic scale20113
NAR Web Server Issue 2011
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tagsalgorithms animal models animals data mining gene expression profiling gene prioritization genes genomics heart humans medline mice orthology relationships text mining zebrafish

Genome SurveyorTool Content

http://veda.cs.uiuc.edu/gs [open in a new window]

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Expression > Gene Regulation
Model Organisms > Fly

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Genome Surveyor 2.0: cis-regulatory analysis in Drosophila20113
NAR Web Server Issue 2011
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tagsanimals binding sites drosophila drosophila melanogaster insect genome transcription factors transcriptional regulatory elements

GLAMMTool Content

http://glamm.lbl.gov [open in a new window]

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Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

GLAMM is a web server for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic data and investigating the construction of novel, transgenic pathways.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
GLAMM: Genome-Linked Application for Metabolic Maps20115
NAR Web Server Issue 2011
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tagsgenomics metabolic networks and pathways

GPU.proton.DOCKTool Content

http://gpudock.orgchm.bas.bg/ [open in a new window]

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Protein > Molecular Dynamics and Docking
Protein > Networks & Interactions, Pathways and Enzymes

Genuine Protein Ultrafast proton equilibria consistent DOCKing (GPU.proton.DOCK) is a tool for in silico prediction of protein-protein interactions via ultrafast docking that considers electrostatic interactions and proton equilibria effects on the docking partners.

This content is being maintained by alexkant.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing.20111
NAR Web Server Issue 2011
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tagsalgorithms fourier analysis multiprotein complexes mutagenesis protein interaction mapping protons static electricity

HapEditTool Content

http://embio.yonsei.ac.kr/hapedit [open in a new window]

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DNA > Mapping and Assembly

HapEdit is a tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2011
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HMMER Web ServerTool Content

http://hmmer.janelia.org [open in a new window]

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Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching and Classification

HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
HMMER web server: interactive sequence similarity searching201124
NAR Web Server Issue 2011
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external linksLink on Twitter Link on Wikipedia
tagsalgorithms computational biology information storage and retrieval internet markov chains protein databases protein sequence analysis sequence alignment software

ICSNPathwayTool Content

http://icsnpathway.psych.ac.cn/ [open in a new window]

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Human Genome > Genomics
Human Genome > Sequence Polymorphisms

ICSNPathway is a web tool for the identification of candidate causal SNPs and their corresponding candidate causal pathways from genome wide association studies. ISCNPathway integrates linkage disequilibrium analysis, functional SNP annotation and pathway based analysis to identify these SNPs and pathways.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework20117
NAR Web Server Issue 2011
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tagsgenome-wide association study humans linkage disequilibrium rheumatoid arthritis single nucleotide polymorphism

inGAP-svTool Content

http://ingap.sourceforge.net [open in a new window]

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DNA > Sequence Polymorphisms

inGAP-sv is a web server to identify and visualize structural variation from paired end mapping data. Several important features including local depth of coverage, mapping quality and associated tandem repeats are used to evaluate the quality of the predicted structural variation.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data20111
NAR Web Server Issue 2011
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tagschromosome aberrations chromosome mapping computer simulation dna sequence analysis genetic variation high-throughput nucleotide sequencing indel mutation

IntFOLDTool Content

http://www.reading.ac.uk/bioinf/IntFOLD/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction20119
NAR Web Server Issue 2011
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tagsbinding sites ligands molecular models protein conformation protein folding protein sequence analysis tertiary protein structure

iPathTool Content

http://pathways.embl.de [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

iPath is a web tool for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
iPath2.0: interactive pathway explorer20115
NAR Web Server Issue 2011
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tagsenzymes genomics metabolic networks and pathways metagenomics

iPBATool Content

http://www.dsimb.inserm.fr/dsimb_tools/ipba/ [open in a new window]

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Protein > 3-D Structure Comparison

iPBA uses specialized protein block substitution matrices and anchor based methodology for pairwise protein structure comparisons.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
iPBA: a tool for protein structure comparison using sequence alignment strategies20113
NAR Web Server Issue 2011
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tagsalgorithms protein conformation protein databases protein sequence analysis sequence alignment

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