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Links tagged with 'animals'

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Found 373 links

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eShadowTool Content

http://eshadow.dcode.org/ [open in a new window]

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Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

A tool for phylogenetic shadowing of multiple sequences from closely related species. This analyses of multiple sequence alignments can be used to predict putative functional elements.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
eShadow: a tool for comparing closely related sequences200464
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tagsanimals computational biology conserved sequence exons genetic databases humans intergenic dna papio peptides proteins software design tertiary protein structure

ESTExplorerTool Content

http://estexplorer.biolinfo.org [open in a new window]

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DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

links directory index: 166
TitlePublication YearGoogle Scholar Citation Count
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform200750
A hitchhiker's guide to expressed sequence tag (EST) analysis2007116
NAR Web Server Issue 2007
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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

euGenes: Genomic Information for Eukaryotic OrganismsDatabase Content

http://iubio.bio.indiana.edu:8089/ [open in a new window]

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Model Organisms > General Resources

Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
euGenes: a eukaryote genome information system200239
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tagsanimals arabidopsis caenorhabditis elegans chromosome mapping database management systems drosophila forecasting genetic databases genome humans mice saccharomyces sequence homology zebrafish

EuPathDB (formerly ApiDB)Database Content

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

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Model Organisms > Databases

EuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. EuPathDB currently supports more than 80 searches. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
EuPathDB: a portal to eukaryotic pathogen databases201039
NAR Database Issue 2010
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tagsanimals computational biology genetic databases humans nucleic acid databases protein databases protozoan genome protozoan infections protozoan proteins tertiary protein structure

EuroPhenomeDatabase Content

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

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Model Organisms > Databases

The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or the predicted phenotype.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
EuroPhenome: a repository for high-throughput mouse phenotyping data201022
NAR Database Issue 2010
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tagsanimals computational biology genetic databases inbred c57bl mice inbred strains mice knockout mice mice phenotype programming languages protein databases tertiary protein structure

FANTOMDatabase Content

http://fantom.gsc.riken.jp/4/ [open in a new window]

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Expression > Databases
Human Genome > Databases

The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation20115
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals cell differentiation gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic transcription genomics humans macrophages mice molecular sequence annotation transcription factors tumor cell line

FANTOM - Functional Annotation of MouseDatabase Content

http://www.gsc.riken.go.jp/e/FANTOM/ [open in a new window]

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Model Organisms > Mouse and Rat

Functional annotations for RIKEN full-length cDNA clones.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Integrated analysis of the genome and the transcriptome by FANTOM20043
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tagsalgorithms animals chromosome mapping database management systems documentation genome mice phylogeny proteome sequence alignment sequence analysis systems integration transcription factors

FASTA ProgramsTool Content

http://fasta.bioch.virginia.edu/ [open in a new window]

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Sequence Comparison > Similarity Searching and Classification

Sequence retrieval and comparison tools.

links directory index: 12295
TitlePublication YearGoogle Scholar Citation Count
Rapid and sensitive sequence comparison with FASTP and FASTA19901956
Improved tools for biological sequence comparison198810339
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tagsadrenergic receptors algorithms amino acid sequence animals antigen receptors base sequence dna eye proteins gene library globins humans information systems molecular sequence data nucleic acid sequence homology peptides proteins rod opsins transforming growth factors

FatiGOplusTool Content

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

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

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

links directory index: 1322
TitlePublication YearGoogle Scholar Citation Count
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments2007150
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments2006215
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments2005204
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes2004753
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs animals artificial intelligence binding sites chromosome mapping computational biology dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny programming languages rats sequence alignment systems biology systems integration transcription factors

FFPredTool Content

http://bioinf.cs.ucl.ac.uk/ffpred/ [open in a new window]

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Protein > Annotation and Function
Protein > Sequence Features

Using a machine learning approach, FFPred server predicts protein function using protein features scanned against a library of over 300 Gene Ontology annotation terms. FFPred has the capacity to annotate distant homologues and orphan protein sequences.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
FFPred: an integrated feature-based function prediction server for vertebrate proteomes200812
NAR Web Server Issue 2008
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tagsanimals humans mice protein sequence analysis proteome systems integration vertebrates

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp [open in a new window]

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Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
FGF: a web tool for Fishing Gene Family in a whole genome database20073
NAR Web Server Issue 2007
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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

Filamentous Fungal Gene Expression Database (FFGED)Database Content

http://bioinfo.townsend.yale.edu/ [open in a new window]

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Expression > Databases
Model Organisms > Databases

The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.

This content is being maintained by Jeffrey P. Townsend.

links directory index: 158
TitlePublication YearGoogle Scholar Citation Count
Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons200741
Enabling a community to dissect an organism: overview of the Neurospora functional genomics project200764
Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination200553
NAR Web Server Issue 2005
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tagsalgorithms amitrole animals base sequence basic-leucine zipper transcription factors bayes theorem ChIP-seq chromosome mapping cluster analysis computational biology computer graphics database management systems dictyostelium dna-binding proteins enzyme inhibitors experimental design expressed sequence tags fungal dna fungal gene expression regulation fungal genes fungal genome fungal proteins fungal spores gene deletion gene expression gene expression profiling gene library genetic databases genetic models genetic promoter regions genetic techniques genetic transcription genomics internet messenger rna microarray molecular sequence data mutation neurospora neurospora crassa northern blotting nucleic acid databases oligonucleotide array sequence analysis oligonucleotide probes phenotype regulon related experiments reproducibility of results rna-seq saccharomyces cerevisiae saccharomyces cerevisiae proteins sequence alignment single nucleotide polymorphism software statistical models systems integration transcription factors user-computer interface ustilago

FlyFactorSurveyDatabase Content

http://pgfe.umassmed.edu/TFDBS/ [open in a new window]

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Model Organisms > Databases

FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system20119
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals bacteria binding sites drosophila drosophila proteins genetic databases transcription factors transcriptional regulatory elements two-hybrid system techniques

FlyTFDatabase Content

http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html [open in a new window]

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Model Organisms > Databases

FlyTF is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. This database contains information on the manual curation of 1052 FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database201012
NAR Database Issue 2010
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tagsanimals computational biology dna drosophila melanogaster drosophila proteins genetic databases genetic transcription nucleic acid databases protein databases tertiary protein structure transcription factors

FooterTool Content

http://biodev.hgen.pitt.edu/Footer/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting200526
NAR Web Server Issue 2005
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tagsalgorithms animals binding sites dna footprinting dna sequence analysis gene expression regulation genetic promoter regions mammals phylogeny transcription factors

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