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InterPro: An integrated documentation resource for protein families, domains and functional sites

2002 Briefings in Bioinformatics  
There are several signature and sequence cluster-based methods for protein classification, each resource having distinct areas of optimum application owing to the differences in the underlying analysis  ...  In recognition of this, InterPro was developed as an integrated documentation resource for protein families, domains and functional sites, to rationalise the complementary efforts of the individual protein  ...  Acknowledgements The InterPro project is supported by the ProFuSe grant (number QLG2-CT-2000-00517) of the European Commission.  ... 
doi:10.1093/bib/3.3.225 pmid:12230031 fatcat:2igbmarmcjbpfphuwf6l7ny4cy

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes

R. Apweiler
2001 Nucleic Acids Research  
The two main projects used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31-67% (InterPro statistics) of the proteins from each of the complete genomes.  ...  The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes  ...  APPLICATIONS OF THE PROTEOME ANALYSIS DATABASE The Proteome Analysis Database provides a perspective on domain structure and function, gene duplication and protein families in different genomes.  ... 
doi:10.1093/nar/29.1.44 pmid:11125045 pmcid:PMC29822 fatcat:ug42g6zpf5bsfoam7zavbsvlki

Integrating Genomic and Proteomic Data: The Integr8 Project

Manuela Pruess, Paul Kersey, Rolf Apweiler
2004 Journal of Integrative Bioinformatics  
The Proteome Analysis database for statistical analysis and the Genome Reviews for annotated genome information are the main developments within the Integr8 project.  ...  With the BioMart application, an interactive querying tool for performing customisable proteome analysis and data mining is offered.  ...  Therefore methods are going to be developed to map protein sequences not annotated in the original EMBL genome entries (which may represent corrected versions of originally annotated protein sequences,  ... 
doi:10.1515/jib-2004-9 fatcat:7m7r4o7yj5h4hki3ep2a3yowzy

The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro

E. Camon
2003 Genome Research  
Article and publication are at  ...  Applications of GOA in Genome Analysis To support the mapping of biological knowledge, and especially to facilitate the interpretation of genomic data, the GOA project annotations have been cross linked  ...  Applications of GOA in Proteome Analysis An application of the GO mappings at the EBI can be seen on the Proteome Analysis pages ( proteome/) produced by the SWISS-PROT group, where  ... 
doi:10.1101/gr.461403 pmid:12654719 pmcid:PMC430163 fatcat:y33clngkn5g2pb7eegoclhgbvq

The European Bioinformatics Institute's data resources

C. Brooksbank
2003 Nucleic Acids Research  
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner.  ...  The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes  ...  The system also provides access to mainstream bioinformatics applications for sequence database searching and protein and nucleic acid sequence analysis.  ... 
doi:10.1093/nar/gkg066 pmid:12519944 pmcid:PMC165513 fatcat:46gy4lg2v5ak7mdns47kaelgpu

The Gene Ontology Annotation (GOA) Project—Application of GO in SWISS-PROT, TrEMBL and InterPro

Evelyn Camon, Daniel Barrell, Catherine Brooksbank, Michele Magrane, Rolf Apweiler
2003 Comparative and Functional Genomics  
Acknowledgements GOA is supported by the European Commission and the US National Institutes of Health.  ...  In the GOA project, this vocabulary is being applied to a non-redundant set of proteins described in the EBI's core genome and proteome databases (SWISS-PROT, TrEMBL and Ensembl [8, 11] that collectively  ...  A slimmed-down version of GO (GO-slim), representing high-level GO terms, provides an overview of each proteome [14] InterPro GO annotations made by InterPro are visible directly in InterPro entries  ... 
doi:10.1002/cfg.235 pmid:18629103 pmcid:PMC2447390 fatcat:ans3bf5ewfcytdlejdkhc6lbya

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study

M. C. Costanzo, J. Park, R. Balakrishnan, J. M. Cherry, E. L. Hong
2011 Database: The Journal of Biological Databases and Curation  
Using this method, we show that comparison of manually assigned 'unknown' annotations in the Saccharomyces Genome Database (SGD) with InterPro-based predictions can identify annotations that need to be  ...  Thus, the combination of manual and computational methods is essential to provide the most accurate and complete functional annotation of a genome.  ...  Reddy, Ralf Stephan, and Kimberly van Auken for assistance in determining counts of genes and annotations in other databases; and all members of the SGD project for helpful discussions and support.  ... 
doi:10.1093/database/bar004 pmid:21411447 pmcid:PMC3067894 fatcat:jaxwcnpsffhahj5n2p7q37g5ka

PCAS--a precomputed proteome annotation database resource

Yong Zhang, Yanbin Yin, Yunjia Chen, Ge Gao, Peng Yu, Jingchu Luo, Ying Jiang
2003 BMC Genomics  
We applied most available motif or domain databases and their analysis methods, including hmmpfam search of HMMs in Pfam, SMART and TIGRFAM, RPS-PSIBLAST search of PSSMs in CDD, pfscan of PROSITE patterns  ...  In addition, signal peptide and TM are predicted using SignalP and TMHMM respectively. We mapped SUPERFAMILY and COGs to InterPro, so the motif or domain databases are integrated through InterPro.  ...  Acknowledgements The authors wish to thank Anders Krogh for kindly providing TMHMM, Beijing Institute of Applied Physics and Computational Mathematics, Computing Center of Peking University for computing  ... 
doi:10.1186/1471-2164-4-42 pmid:14594458 pmcid:PMC293463 fatcat:oiysgeeuczgelmf52rcas7yuwm

Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes

Lorna J Richardson, Neil D Rawlings, Gustavo A Salazar, Alexandre Almeida, David R Haft, Gregory Ducq, Granger G Sutton, Robert D Finn
2018 Nucleic Acids Research  
Automatic annotation of protein function is routinely applied to newly sequenced genomes.  ...  While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge Peter Karp for help and support with the incorporation of MetaCyc data into Genome Properties. FUNDING  ... 
doi:10.1093/nar/gky1013 pmid:30364992 fatcat:cfganwexh5b5dhq53n2xzypxv4

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation

S. Burge, E. Kelly, D. Lonsdale, P. Mutowo-Muellenet, C. McAnulla, A. Mitchell, A. Sangrador-Vegas, S.-Y. Yong, N. Mulder, S. Hunter
2012 Database: The Journal of Biological Databases and Curation  
The InterPro2GO mappings are comprised of the cross-references between these two resources and are the largest source of GO annotation predictions for proteins.  ...  We discuss the unique challenges involved in integrating specific GO terms with entries that may describe a diverse set of proteins, and we illustrate, with examples, how InterPro hierarchies reflect GO  ...  Acknowledgements We thank Emily Dimmer and Claire O'Donovan for their critical reading of this manuscript and Tony Sawford for assistance with protein match counts. Conflict of interest.  ... 
doi:10.1093/database/bar068 pmid:22301074 pmcid:PMC3270475 fatcat:mczeyk6qqrhxpn2aysoyqgocde

Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists

Marco Masseroli, Elisa Bellistri, Andrea Franceschini, Francesco Pinciroli
2007 BMC Bioinformatics  
Results: Exploiting protein information in Pfam and InterPro databanks, we developed and added in GFINDer original modules specifically devoted to the exploration and analysis of functional signatures  ...  In particular, when uploaded nucleotide sequence identifiers are subdivided in classes, the Statistics Protein Families&Domains module allows estimating relevance of Pfam or InterPro controlled annotations  ...  Acknowledgements The authors thank Andrea Maffezzoli for his contribution in writing this manuscript. This article has been published as part of BMC Bioinformatics  ... 
doi:10.1186/1471-2105-8-s1-s14 pmid:17430558 pmcid:PMC1885843 fatcat:odsdeaohbjd27pdvxgwrohjemu

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

R. Apweiler
2001 Nucleic Acids Research  
Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1 000 000 hits from 462 500 proteins in SWISS-PROT and TrEMBL).  ...  InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects.  ...  ACKNOWLEDGEMENTS The InterPro project is supported by grant number BIO4-CT98-0052 of the European Commission. T.K.A. is a Royal Society University Research Fellow.  ... 
doi:10.1093/nar/29.1.37 pmid:11125043 pmcid:PMC29841 fatcat:ft4lb3l2zjhnph2ll42i3jnz3e

PhenoFam-gene set enrichment analysis through protein structural information

Maciej Paszkowski-Rogacz, Mikolaj Slabicki, M Teresa Pisabarro, Frank Buchholz
2010 BMC Bioinformatics  
Results: PhenoFam performs gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms.  ...  annotation of genes.  ...  Acknowledgements This work was supported by the Max Planck Society, the Bundesministerium für Bildung und Forschung grant NGFN-Plus (01GS0859), the Deutsche Forschungsgemeinschaft (SFB 655 'Cells into tissues') and  ... 
doi:10.1186/1471-2105-11-254 pmid:20478033 pmcid:PMC2881086 fatcat:sbhd2pkpxjhmnmbgywr54fmv54

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes

M. Pruess
2003 Nucleic Acids Research  
Three main projects are used, InterPro, CluSTr and GO Slim, to give an overview on families, domains, sites, and functions of the proteins from each of the complete genomes.  ...  protein coding sequences of the complete genomes of bacteria, archeae and eukaryotes.  ...  DATABASE APPLICATIONS AND DATA PRESENTATION The Proteome Analysis database provides information on domain structure and function, gene duplication and protein families in different genomes.  ... 
doi:10.1093/nar/gkg105 pmid:12520037 pmcid:PMC165552 fatcat:jnlpvwyqfrbznjhi4ug6zpkt7a
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