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Links tagged with 'humans'

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Found 267 links

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3D-JuryTool Content

http://meta.bioinfo.pl/submit_wizard.pl [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

links directory index: 775
TitlePublication YearGoogle Scholar Citation Count
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure2003115
3D-Jury: a simple approach to improve protein structure predictions2003592
Detection of reliable and unexpected protein fold predictions using 3D-Jury200368
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology computer simulation database management systems humans molecular models protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment tertiary protein structure

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html [open in a new window]

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

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures20073
Query3d: a new method for high-throughput analysis of functional residues in protein structures200536
A structural study for the optimisation of functional motifs encoded in protein sequences20047
Three-dimensional profiles: a new tool to identify protein surface similarities199852
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

AD-ENMTool Content

http://enm.lobos.nih.gov [open in a new window]

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Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

links directory index: 256
TitlePublication YearGoogle Scholar Citation Count
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin200545
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved200552
Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model200559
A comparative study of motor-protein motions by using a simple elastic-network model2003100
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tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

ADGOTool Content

http://www.btool.org/ADGO2 [open in a new window]

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Expression > Gene Set Analysis
Expression > cDNA, EST, SAGE

ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
ADGO 2.0: interpreting microarray data and list of genes using composite annotations.20113
ADGO: analysis of differentially expressed gene sets using composite GO annotation200625
NAR Web Server Issue 2011
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tagsalgorithms animals biological models cell differentiation computer simulation documentation gene expression profiling genes humans mice molecular sequence annotation oligonucleotide array sequence analysis protein databases proteins rats t-lymphocytes

AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/ [open in a new window]

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DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
AGenDA: gene prediction by cross-species sequence comparison200411
NAR Web Server Issue 2004
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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

ALEXA-seqTool Content

http://www.alexaplatform.org/alexa_seq/ [open in a new window]

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Expression > Splicing
Expression > Transcript Expression Analysis
RNA > Functional RNAs
RNA > General Resources

A method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms. Provides alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis.

This content is being maintained by mgriffit.

links directory index: 36
TitlePublication YearGoogle Scholar Citation Count
Alternative expression analysis by RNA sequencing201036
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tagsalternative splicing antineoplastic antimetabolites colorectal neoplasms expressed sequence tags fluorouracil gene expression gene expression profiling genetic databases humans messenger rna neoplasm drug resistance next-generation sequencing oligonucleotide array sequence analysis protein isoforms reverse transcriptase polymerase chain reaction rna sequence analysis rna-seq RNAseq sequence alignment tumor cell line whole transcriptome shotgun sequencing

ALGGENTool Content

http://alggen.lsi.upc.es/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters200640
FibreHelix, a program for calculating the X-ray diffraction pattern of macromolecules with helical symmetry: application to DNA coiled coils20052
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences20036
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN2003107
PROMO: detection of known transcription regulatory elements using species-tailored searches2002121
NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

AnnotQTLTool Content

http://annotqtl.genouest.org [open in a new window]

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DNA > Annotations
DNA > Gene Prediction

AnnotQTL is a web tool for gathering functional and comparative information on a genomic region. It is designed to aggregate functional annotations from different websites by minimizing the redundancy of the information.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
AnnotQTL: a new tool to gather functional and comparative information on a genomic region20111
NAR Web Server Issue 2011
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tagsanimals cattle genomics humans livestock mice molecular sequence annotation quantitative trait loci

Apollo Genome Annotation and Curation ToolTool Content

http://apollo.berkeleybop.org [open in a new window]

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DNA > Annotations
Human Genome > Annotations

Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.

This content is being maintained by suzi.

links directory index: 279
TitlePublication YearGoogle Scholar Citation Count
Apollo: a sequence annotation editor2002279
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tagsanimals database management systems humans nucleic acid databases software design

Argonne National Laboratory - Computational Biology DatabasesTool Content

http://www-unix.mcs.anl.gov/compbio/index.html [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.

links directory index: 833
TitlePublication YearGoogle Scholar Citation Count
Sentra, a database of signal transduction proteins200216
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction2000369
MPW: the Metabolic Pathways Database1998127
Searching for patterns in genomic data1997221
The metabolic pathway collection from EMP: the enzymes and metabolic pathways database1996100
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tagsanimals bacteria biological transport chemotaxis conserved sequence enzymes eukaryota factual databases fungi genome humans metabolism methylation multigene family open reading frames phosphorylation prokaryotic cells protein databases protein kinases protein-serine-threonine kinases proteins sequence homology signal transduction systems integration tertiary protein structure

ArrayProspectorTool Content

http://string32.embl-heidelberg.de:8080/prophecies_html/prophecies.html [open in a new window]

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Expression > Transcript Expression Analysis

ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
ArrayProspector: a web resource of functional associations inferred from microarray expression data200421
NAR Web Server Issue 2004
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tagsalgorithms animals gene expression profiling humans oligonucleotide array sequence analysis proteins reproducibility of results

ArrayTrackTool Content

http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/ [open in a new window]

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Expression > Transcript Expression Analysis

ArrayTrack™ provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. Specifically, ArrayTrack™ is MIAME (Minimum Information About A Microarray Experiment)-supportive for storing both microarray data and experiment parameters associated with a pharmacogenomics or toxicogenomics study.

links directory index: 132
TitlePublication YearGoogle Scholar Citation Count
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research2003132
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tagsfactual databases gene library humans oligonucleotide array sequence analysis protein array analysis public health informatics public sector reference values statistics as topic toxicogenetics toxicology united states united states food and drug administration

ASePCRTool Content

http://genome.ewha.ac.kr/ASePCR/ [open in a new window]

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DNA > Tools For the Bench
Expression > Splicing

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs200510
NAR Web Server Issue 2005
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tagsalgorithms alternative splicing animals base sequence expressed sequence tags humans messenger rna mice molecular sequence data rats reverse transcriptase polymerase chain reaction tissue distribution

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/ [open in a new window]

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Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences200424
NAR Web Server Issue 2004
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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

AStalavistaTool Content

http://genome.imim.es/astalavista/ [open in a new window]

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Expression > Splicing

AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets200716
NAR Web Server Issue 2007
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tagsalternative splicing chromosome mapping computational biology dna probes dna sequence analysis genetic databases genome humans messenger rna oligonucleotide array sequence analysis rna splice sites

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