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Links tagged with 'multigene family'

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Found 13 links

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BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

DNA > Gene Prediction
Model Organisms > Microbes

BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

NAR Web Server Issue 2006
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tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

CiFDatabase Content

http://www.fusariumdb.org/

Model Organisms > Databases

The Cyber infrastructure for Fusarium (CiF) consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. The FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them using multiple tools without requiring repeated copying-and-pasting of sequences.

NAR Database Issue 2011
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tagsfungal genome fungal proteins fusarium genetic databases genomics multigene family phylogeny systems integration

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

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.

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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

H-InvDBDatabase Content

http://www.h-invitational.jp/

Human Genome > Databases

The H-Invitational Database (H-InvDB) is a comprehensive annotation resource of human genes and transcripts. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs.

This content is being maintained by cyamasak.

NAR Database Issue 2010
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tagsalternative splicing complementary dna computational biology genes genetic databases genetic models genetic polymorphism human genome humans messenger rna microsatellite repeats multigene family nucleic acid databases oligonucleotide array sequence analysis open reading frames single nucleotide polymorphism tertiary protein structure

IPI - International Protein IndexTool Content

http://www.ebi.ac.uk/IPI/

Protein > Sequence Data

IPI provides a top level view of the human, mouse and rat proteome data found in Swiss-Prot, TrEMBL, RefSeq and Ensembl.

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tagsanimals computational biology humans international cooperation mice multigene family proteins proteome proteomics rats

iSPOTTool Content

http://cbm.bio.uniroma2.it/ispot/

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence animals binding sites computational biology factual databases humans ligands molecular models molecular sequence data multigene family peptide fragments peptide library probability protein binding protein databases protein sequence analysis proteins sequence alignment src homology domains substrate specificity tertiary protein structure

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence homology animals archaeal genome bacterial genome computational biology conserved sequence dna footprinting dna sequence analysis fish proteins fos genes genetic promoter regions genomics growth hormone humans insulin interleukin-3 introns metallothionein multigene family myc genes nucleic acid databases nucleic acid regulatory sequences nucleic acid sequence homology phylogeny regulator genes transcriptional regulatory elements

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2003NAR Web Server Issue 2006NAR Web Server Issue 2007
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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

SH3-HunterTool Content

http://cbm.bio.uniroma2.it/SH3-Hunter/

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.

This content is being maintained by enricoferraro.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals artificial intelligence automated pattern recognition binding sites chemical models computational biology computer simulation factual databases humans ligands molecular models molecular sequence data multigene family neural networks (computer) peptide fragments peptide library peptides probability protein binding protein interaction mapping protein sequence analysis proteins proteome sensitivity and specificity sequence alignment src homology domains structure-activity relationship substrate specificity tertiary protein structure

STAMPTool Content

http://www.benoslab.pitt.edu/stamp/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.

NAR Web Server Issue 2007
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tagsamino acid motifs animals base sequence binding sites cluster analysis computational biology dna dna sequence analysis humans molecular sequence data multigene family protein binding saccharomyces cerevisiae sequence alignment transcription factors

TraFaCTool Content

http://trafac.cchmc.org/trafac/index.jsp

Expression > Gene Regulation
Sequence Comparison > Comparative Genomics

TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions using a comparative sequence analysis approach.

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tagsanimals base composition binding sites brain chemistry cd4 antigens conserved sequence dna helicases dna-binding proteins gene expression profiling genetic databases genetic promoter regions humans intestines lung mice multigene family nucleic acid regulatory sequences organ specificity proteins transcription factors untranslated rna xeroderma pigmentosum group d protein

TreeDetTool Content

http://treedetv2.bioinfo.cnio.es/treedet/index.html

Protein > Annotation and Function
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence conserved sequence cyclins gtp-binding proteins molecular models molecular sequence data multigene family phylogeny protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins p21(ras) sequence alignment structure-activity relationship tertiary protein structure theoretical models

Viral BioinformaticsTool Content

http://athena.bioc.uvic.ca/

Model Organisms > Other Organisms
Protein > Sequence Features
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Viral Bioinformatics provides access to viral genomes and a variety of tools for comparative genomic analyses.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome base composition base sequence biological models canada capripoxvirus chlamydophila pneumoniae cluster analysis computational biology computer systems database management systems dna dna sequence analysis documentation factual databases fuzzy logic genetic databases genome genomics humans molecular evolution molecular sequence data multigene family multimedia mutation nucleic acid databases nucleic acid regulatory sequences nucleotides open reading frames phylogeny poxviridae programming languages protein databases protein sequence analysis reference standards sequence alignment statistical data interpretation systems integration technology transfer thermoplasma vaccinia virus variola virus viral dna viral genes viral genome viral proteins