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Links tagged with 'animals'

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Found 373 links

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CIPRO 2.5Database Content

http://cipro.ibio.jp/2.5 [open in a new window]

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Model Organisms > Databases

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The CIPRO database collects published data as well as unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data. Homologs in humans and major model organisms are included. Annotations are open to evaluation by users through the CIPRO website.

This content is being maintained by tendo.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality20116
NAR Database Issue 2011
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tagsamino acid sequence animals ciona intestinalis computational biology gene expression profiling genomics molecular sequence annotation protein databases proteome proteomics systems integration

cisREDDatabase Content

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

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

cisRED is a database system for genome-scale computational discovery of regulatory elements.

links directory index: 74
TitlePublication YearGoogle Scholar Citation Count
cisRED: a database system for genome-scale computational discovery of regulatory elements200674
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tagsanimals computational biology genetic promoter regions genomics nucleic acid databases response elements

CisRegTestTool Content

http://www.moseslab.csb.utoronto.ca/alan/cis_reg_test.html [open in a new window]

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Protein > 3-D Structural Features

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites20099
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tagsanimals binding sites drosophila drosophila melanogaster drosophila proteins genetic models genetic selection nucleic acid regulatory sequences transcription factors
setsUniversity of Toronto

ClanToxTool Content

http://www.clantox.cs.huji.ac.il [open in a new window]

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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.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
ClanTox: a classifier of short animal toxins20094
NAR Web Server Issue 2009
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tagsanimals biological toxins cysteine protein sequence analysis proteomics

CLIPZDatabase Content

http://www.clipz.unibas.ch [open in a new window]

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RNA > Databases

CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The CLIPZ platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets.

This content is being maintained by nonb@nih.gov.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins201110
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals binding sites genetic databases genome humans messenger rna mice rna sequence analysis rna-binding proteins transfer rna untranslated rna

ClotbaseDatabase Content

http://www.clotbase.bicnirrh.res.in/ [open in a new window]

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Protein > Databases

ClotBase is a curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases , mutation and links to external databases

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
ClotBase: a knowledgebase on proteins involved in blood coagulation.20100
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tagsamino acid sequence animals blood coagulation blood coagulation disorders blood coagulation factors blood proteins consensus sequence factual databases genetic databases humans molecular sequence data mutation mutation prediction mutations protein conformation protein databases proteins sequence alignment

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/ [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

links directory index: 3211
TitlePublication YearGoogle Scholar Citation Count
The COG database: new developments in phylogenetic classification of proteins from complete genomes20011177
A genomic perspective on protein families19972034
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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

CompareProspectorTool Content

http://compareprospector.stanford.edu/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

links directory index: 164
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
Eukaryotic regulatory element conservation analysis and identification using comparative genomics2004132
NAR Web Server Issue 2004
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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

ComSinDatabase Content

http://antares.protres.ru/comsin/. [open in a new window]

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Protein > Databases

ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder20108
NAR Database Issue 2010
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tagsanimals bacterial proteins computational biology genetic databases humans molecular conformation molecular models protein binding protein conformation protein databases tertiary protein structure

CONREALTool Content

http://conreal.niob.knaw.nl/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

links directory index: 125
TitlePublication YearGoogle Scholar Citation Count
CONREAL web server: identification and visualization of conserved transcription factor binding sites200541
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting200484
NAR Web Server Issue 2005
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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

ConsensusPathDBDatabase Content

http://cpdb.molgen.mpg.de [open in a new window]

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Human Genome > Databases
Model Organisms > Databases
Protein > Databases

ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
ConsensusPathDB: toward a more complete picture of cell biology201115
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals factual databases gene expression gene regulatory networks genetic databases humans metabolic networks and pathways mice protein interaction mapping signal transduction

ConsiteTool Content

http://www.phylofoot.org/consite/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

links directory index: 514
TitlePublication YearGoogle Scholar Citation Count
ConSite: web-based prediction of regulatory elements using cross-species comparison2004250
Identification of conserved regulatory elements by comparative genome analysis2003264
NAR Web Server Issue 2004
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tagsalgorithms animals binding sites computational biology conserved sequence dna dna footprinting dna sequence analysis genetic models human genome humans nucleic acid regulatory sequences phylogeny predictive value of tests regulator genes sensitivity and specificity sequence alignment transcription factors

CoPubTool Content

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

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Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics

CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
CoPub: a literature-based keyword enrichment tool for microarray data analysis200833
NAR Web Server Issue 2008NAR Web Server Issue 2011
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tagsanimals gene expression profiling humans medline mice oligonucleotide array sequence analysis rats

CORUMDatabase Content

http://mips.gsf.de/genre/proj/corum [open in a new window]

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Protein > Databases

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). The CORUM dataset is built from 3198 different genes, representing approximately 16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. A 'Phylogenetic Conservation' analysis tool allows one to predict the occurrence of protein complexes in different phylogenetic groups.

links directory index: 116
TitlePublication YearGoogle Scholar Citation Count
CORUM: the comprehensive resource of mammalian protein complexes--20092010116
NAR Database Issue 2010
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tagsanimals computational biology genetic databases humans mice multiprotein complexes phylogeny protein databases rats saccharomyces cerevisiae tertiary protein structure

COXPRESdbDatabase Content

http://coxpresdb.jp [open in a new window]

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Expression > Databases
Model Organisms > Databases

COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
COXPRESdb: a database to compare gene coexpression in seven model animals201113
NAR Database Issue 2011
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external linksLink on Twitter
tagsanimal models animals gene expression gene expression profiling gene regulatory networks genetic databases humans mice protein interaction mapping rats

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