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InterPro, progress and status in 2005

by Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Er Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer Mcdowall, Alex Mitchell, Anastasia N. Nikolskaya, Ra Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu - Nucleic Acids Res , 2005
"... InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into Inte ..."
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InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated

GFam: a platform for automatic annotation of gene families

by Rajkumar Sasidharan, David Swarbreck, Eva Huala, Alberto Paccanaro , 2011
"... We have developed GFam, a platform for automatic annotation of gene/protein families. GFam provides a framework for genome initiatives and model organism resources to build domain-based families, derive meaningful functional labels and offers a seamless approach to propagate functional annotation ac ..."
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across periodic genome updates. GFam is a hybrid approach that uses a greedy algorithm to chain component domains from InterPro annotation provided by its 12 member resources followed by a sequence-based connected component analysis of un-annotated sequence regions to derive consensus domain archi

PMID: 15608177

by Status In, Nicola J, Et Al, Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Er Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer Mcdowall, Alex Mitchell, Anastasia N. Nikolskaya, Ra Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu
"... InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into Inte ..."
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InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated

MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res

by Dawn Cotter, Purnima Guda, Eoin Fahy, Shankar Subramaniam , 2004
"... MitoProteome is an object-relational mitochondrial protein sequence database and annotation system. The initial release contains 847 human mitochondrial protein sequences, derived from public sequence databases and mass spectrometric analysis of highly puri®ed human heart mitochondria. Each sequence ..."
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from MINT and DIP; functional domain information from Pfam; protein ®ngerprints from PRINTS; protein family and family-speci®c signatures from InterPro; structure data from PDB; mutation data from PMD; BLAST homology data from NCBI NR; and proteins found to be related based on LocusLink and SWISS

DOI: 10.1093/nar/gkg128 The TIGRFAMs database of protein families

by Daniel H. Haft, Jeremy D. Selengut, Owen White , 2002
"... TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature references and pointers to related TIGRFAMs, Pfam and InterPro models. These models are designed to support bo ..."
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TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature references and pointers to related TIGRFAMs, Pfam and InterPro models. These models are designed to support

Transcriptomics of a Giant Freshwater Prawn (Macrobrachium rosenbergii): De Novo Assembly, Annotation and Marker Discovery

by Hyungtaek Jung, Russell E. Lyons, Hung Dinh, David A. Hurwood, Sean Mcwilliam, Peter B
"... Background: Giant freshwater prawn (Macrobrachium rosenbergii or GFP), is the most economically important freshwater crustacean species. However, as little is known about its genome, 454 pyrosequencing of cDNA was undertaken to characterise its transcriptome and identify genes important for growth. ..."
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members of several biological pathways potentially important for growth. The top InterProScan domains detected included RNA recognition motifs, serine/threonine-protein kinase-like domains, actin-like families, and zinc finger domains. Transcripts derived from genes such as actin, myosin heavy and light

PROCEEDINGS Open Access A domain-centric solution to functional genomics via dcGO Predictor

by Hai Fang, Julian Gough
"... Background: Computational/manual annotations of protein functions are one of the first routes to making sense of a newly sequenced genome. Protein domain predictions form an essential part of this annotation process. This is due to the natural modularity of proteins with domains as structural, evolu ..."
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. This generalized framework we have presented has also been applied to other domain classifications such as InterPro and Pfam, and other ontologies such as mammalian phenotype and disease ontology. The dcGO and its predictor are available at

*Correspondence to:

by Christopher Southan, C. Southan, Bioinformatics Target, Discovery Smithkline Beecham, Pharmaceuticals Newfrontiers, John Wiley , 2000
"... The family and motif databases, PROSITE, PRINTS, Pfam and ProDom, have been integrated into a powerful resource for protein secondary annotation.As of June 2000, InterPro had processed 384 572 proteins in SWISS-PROT and TrEMBL.Because the contributing databases have different clustering principles a ..."
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The family and motif databases, PROSITE, PRINTS, Pfam and ProDom, have been integrated into a powerful resource for protein secondary annotation.As of June 2000, InterPro had processed 384 572 proteins in SWISS-PROT and TrEMBL.Because the contributing databases have different clustering principles

Characterization of the preprotein and amino acid transporter gene family in Arabidopsis. Plant Physiol. 143

by Monika W. Murcha, Dina Elhafez, Ryan Lister, Manuela Baumgartner, Chris Carrie, Dejana Mokranjac, James Whelan , 2007
"... Seventeen loci encode proteins of the preprotein and amino acid transporter family in Arabidopsis (Arabidopsis thaliana). Some of these genes have arisen from recent duplications and are not in annotated duplicated regions of the Arabidopsis genome. In comparison to a number of other eukaryotic orga ..."
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Seventeen loci encode proteins of the preprotein and amino acid transporter family in Arabidopsis (Arabidopsis thaliana). Some of these genes have arisen from recent duplications and are not in annotated duplicated regions of the Arabidopsis genome. In comparison to a number of other eukaryotic

Homology Modeling and Functional Characterization of PR-1a Protein of Hordeum

by Vulgare Subsp Vulgare, Vahid Aslanzadeh, Mostafa Ghaderian , 2012
"... Pathogenesis-related protein 1a of Hordeum vulgare subsp. Vulgare (HvPR-1a) is induced by various pathogens and stress related factors. It plays important roles in plant defense system. Since the discovery of HvPR-1a a great deal of research has been focused on its isolation and characterization. Ho ..."
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annotation of the model carried out with Expasy’s ProtParam server and three different conserved domain finding programs including InterProScan, Proteins Families Database (Pfam), and NCBI Conserved Domains Database (NCBI-CDD). Applying validation programs revealed that the model has good quality
Results 1 - 10 of 15