> Tag > Links tagged with 'multigene family'

Links tagged with 'multigene family'

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV

Found 13 links

Displaying 13 links

Hide Resources (1)Hide Databases (5)Hide Tools (7)

Argonne National Laboratory - Computational Biology DatabasesTool Content

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

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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

BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php [open in a new window]

Share This Link
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.

links directory index: 48
TitlePublication YearGoogle Scholar Citation Count
BAGEL: a web-based bacteriocin genome mining tool200648
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

CiFDatabase Content

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

Share This Link
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.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing20116
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsfungal genome fungal proteins fusarium genetic databases genomics multigene family phylogeny systems integration

COGsTool Content

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

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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

Genome Biology Release 3 of the Drosophila genomeResource Content

http://genomebiology.com/series/drosophila [open in a new window]

Share This Link
Model Organisms > Fly

A series of refereed research articles describing Release 3 of the Drosophila genome are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies.

links directory index: 1971
TitlePublication YearGoogle Scholar Citation Count
Systematic determination of patterns of gene expression during Drosophila embryogenesis2002340
Computational analysis of core promoters in the Drosophila genome20023
Apollo: a sequence annotation editor2002279
An integrated computational pipeline and database to support whole-genome sequence annotation200241
A Drosophila full-length cDNA resource2002148
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence2002275
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome2002125
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly2002168
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective2002313
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review2002279
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence animals base composition base sequence cluster analysis complementary dna computational biology computer-assisted image processing conserved sequence contig mapping database management systems developmental gene expression regulation dna sequence analysis dna transposable elements drosophila drosophila melanogaster drosophila proteins euchromatin expressed sequence tags forecasting gene dosage gene expression profiling gene rearrangement genetic databases genetic promoter regions genetic variation genome heterochromatin humans in situ hybridization insect genes insertional mutagenesis messenger rna molecular evolution molecular sequence data multigene family nucleic acid conformation nucleic acid databases oligonucleotide array sequence analysis physical chromosome mapping protein databases research design software design software validation species specificity transcription initiation site untranslated regions x chromosome

H-InvDBDatabase Content

http://www.h-invitational.jp/ [open in a new window]

Share This Link
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.

links directory index: 298
TitlePublication YearGoogle Scholar Citation Count
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts201011
Integrative annotation of 21,037 human genes validated by full-length cDNA clones2004287
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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/ [open in a new window]

Share This Link
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.

links directory index: 552
TitlePublication YearGoogle Scholar Citation Count
The International Protein Index: an integrated database for proteomics experiments2004552
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals computational biology humans international cooperation mice multigene family proteins proteome proteomics rats

iSPOTTool Content

http://cbm.bio.uniroma2.it/ispot/ [open in a new window]

Share This Link
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and 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.

links directory index: 99
TitlePublication YearGoogle Scholar Citation Count
iSPOT: A web tool to infer the interaction specificity of families of protein modules200325
SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family200074
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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 [open in a new window]

Share This Link
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.

links directory index: 598
TitlePublication YearGoogle Scholar Citation Count
MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes200623
FootPrinter: A program designed for phylogenetic footprinting2003161
Algorithms for phylogenetic footprinting2002146
Discovery of regulatory elements by a computational method for phylogenetic footprinting2002268
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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

PfamDatabase Content

http://pfam.sanger.ac.uk/ [open in a new window]

Share This Link
Protein > Databases

Pfam is a database of protein families and domains. The database uses HMMER3, the latest version of the popular profile hidden Markov model package. Pfam release 24.0 contains 11,912 families.

links directory index: 11859
TitlePublication YearGoogle Scholar Citation Count
The Pfam protein families database.2012212
The Pfam protein families database.20101375
The Pfam protein families database.20081524
Pfam: clans, web tools and services.20061648
The Pfam protein families database.20042639
The Pfam protein families database.20022079
The Pfam protein families database.20001281
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.1999545
Pfam: multiple sequence alignments and HMM-profiles of protein domains.1998556
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Twitter Link on Wikipedia
tagsalgorithms amino acid sequence amino acid sequence homology animals archaeal genome binding sites caenorhabditis elegans computational biology computer communication networks computer graphics encyclopedias as topic factual databases fungal genome genome genomics humans information storage and retrieval internet macromolecular substances markov chains molecular evolution molecular models molecular sequence data multigene family nucleic acid databases phylogeny protein conformation protein databases protein sequence analysis proteins quality control secondary protein structure sequence alignment software statistics as topic tertiary protein structure user-computer interface

SH3-HunterTool Content

http://cbm.bio.uniroma2.it/SH3-Hunter/ [open in a new window]

Share This Link
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

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

This content is being maintained by enricoferraro.

links directory index: 102
TitlePublication YearGoogle Scholar Citation Count
SH3-Hunter: discovery of SH3 domain interaction sites in proteins200711
A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity200617
SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family200074
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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

SilkDBDatabase Content

http://silkworm.genomics.org.cn/ [open in a new window]

Share This Link
Model Organisms > Databases

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently.

links directory index: 45
TitlePublication YearGoogle Scholar Citation Count
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology201045
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals bombyx computational biology expressed sequence tags genetic databases genomics humans multigene family nucleic acid databases oligonucleotide array sequence analysis protein databases

TreeDetTool Content

http://treedetv2.bioinfo.cnio.es/treedet/index.html [open in a new window]

Share This Link
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.

links directory index: 548
TitlePublication YearGoogle Scholar Citation Count
TreeDet: a web server to explore sequence space200624
SQUARE--determining reliable regions in sequence alignments200452
Automatic methods for predicting functionally important residues2003154
A method to predict functional residues in proteins1995318
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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

Associated Tag Cloud