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Links tagged with 'documentation'

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Found 17 links

Displaying 15 links

ADGOTool Content

http://www.btool.org/ADGO2

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.

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

AliasServerDatabase Content

http://cbi.labri.fr/outils/alias/

DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

DIALTool Content

http://caps.ncbs.res.in/DIAL/home.html

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

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

NAR Web Server Issue 2005
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tagsalgorithms amino acid motifs amino acid sequence amino acids aspartic acid endopeptidases calmodulin chemical models cluster analysis database management systems documentation factual databases hydroxymethylbilane synthase molecular models molecular sequence data molecular structure papain porins protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment tertiary protein structure x-ray crystallography

FANTOM - Functional Annotation of MouseDatabase Content

http://www.gsc.riken.go.jp/e/FANTOM/

Model Organisms > Mouse and Rat

Functional annotations for RIKEN full-length cDNA clones.

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tagsalgorithms animals chromosome mapping database management systems documentation genome mice phylogeny proteome sequence alignment sequence analysis systems integration transcription factors

GelScape and GelBankTool Content

http://www.gelscape.ualberta.ca/

Expression > Protein Expression
Protein > Protein Expression

GelScape is a platform-independent 1D and 2D gel analysis system that is freely available. Features include the ability to mark spots, to measure spot intensities and to archive gel images and annotations to the public database GelBank. Includes searchable access to GelBank\'s repository.

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tagsdatabase management systems documentation factual databases gel electrophoresis online systems polyacrylamide gel electrophoresis

GPSDBDatabase Content

http://biomint.pharmadm.com/

Literature > Search Tools
Literature > Text Mining and Semantics

Gene and Protein Synonym DataBase (GPSDB) is a collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms.

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tagscontrolled vocabulary database management systems documentation information dissemination medline natural language processing protein databases proteins terminology as topic

KAASTool Content

http://www.genome.jp/kegg/kaas/

DNA > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

NAR Web Server Issue 2007
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tagsanimals artificial intelligence automation chromosome mapping computational biology controlled vocabulary database management systems documentation genome humans proteome sequence analysis signal transduction

KOBASTool Content

http://kobas.cbi.pku.edu.cn

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

MutDBDatabase Content

http://www.mutdb.org/

DNA > Annotations
DNA > Sequence Polymorphisms

MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.

NAR Web Server Issue 2005
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tagsamino acid substitution database management systems documentation genetic databases genetic predisposition to disease genetic variation human genome humans molecular models mutation phenotype protein conformation protein databases protein sequence analysis proteins sequence alignment single nucleotide polymorphism structure-activity relationship

ORegAnnoDatabase Content

http://www.oreganno.org/

DNA > Annotations
DNA > Databases
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

The Open REGulatory ANNOtation database (ORegAnno) is a collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.

This content is being maintained by obigriffith.

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tagsanimals binding sites database management systems documentation gene expression regulation genetic databases genetic promoter regions genetic variation humans natural language processing nucleic acid databases periodicals as topic protein binding transcription factors transcriptional regulatory elements

PEDRoTool Content

http://pedrodownload.man.ac.uk/

Protein > Proteomics

Software and schemata for modelling, capturing and disseminating proteomics experimental data

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tagsdatabase management systems documentation genetic databases information dissemination molecular models natural language processing programming languages protein conformation protein databases protein sequence analysis proteins proteomics software design

PhenomicDBDatabase Content

http://www.phenomicdb.de/

Model Organisms > General Resources
Protein > Annotation and Function
Sequence Comparison > Comparative Genomics

PhenomicDB integrates the genotype and phenotype information of several organisms from public data sources. The mapping of phenotypic data fields allows cross-species phenotype comparison.

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tagsanimals documentation gene expression profiling genetic databases genomics genotype humans information dissemination phenotype species specificity

POLYVIEW-MMTool Content

http://polyview.cchmc.org/conform.html

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

POLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization.

NAR Web Server Issue 2010
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tagsalgorithms capsid proteins documentation molecular dynamics simulation molecular models peptides protein conformation protein databases protein interaction mapping protein sequence analysis proteins tertiary protein structure

Proteios - The Open Source Proteomics InitiativeTool Content

http://www.proteios.org/

Protein > Proteomics

Proteios is an initiative to create an open-source storage, analysis and organization system for proteomics experiments.

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tagsdatabase management systems documentation electrophoresis information dissemination liquid chromatography mass spectrometry molecular models protein array analysis protein conformation protein databases protein sequence analysis proteins proteomics software design statistical data interpretation

Servers at University College LondonTool Content

http://bioinf.cs.ucl.ac.uk/web_servers/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models