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Nucleic Acids Research Advance Access published online on June 3, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp462
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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ProGMap: an integrated annotation resource for protein orthology

Arnold Kuzniar1, Ke Lin1, Ying He1, Harm Nijveen1, Sándor Pongor2,3 and Jack A. M. Leunissen1,*

1Laboratory of Bioinformatics, Wageningen University and Research Centre (WUR), Dreijenlaan 3, 6703 HA Wageningen, The Netherlands, 2Protein Structure and Bioinformatics Group, International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste, Italy and 3Biological Research Center of Hungarian Academy Sciences, Temesvári krt 62, H-6726 Szeged, Hungary

*To whom correspondence should be addressed. Tel: +31 317 484 074; Fax: +31 317 418 094; Email: jack.leunissen{at}wur.nl

Received January 31, 2009. Revised April 30, 2009. Accepted May 16, 2009.

Current protein sequence databases employ different classification schemes that often provide conflicting annotations, especially for poorly characterized proteins. ProGMap (Protein Group Mappings, http://www.bioinformatics.nl/progmap) is a web-tool designed to help researchers and database annotators to assess the coherence of protein groups defined in various databases and thereby facilitate the annotation of newly sequenced proteins. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences which is mapped to 240 000 protein group descriptions collected from UniProt, RefSeq, Ensembl, COG, KOG, OrthoMCL-DB, HomoloGene, TRIBES and PIRSF. ProGMap combines the underlying classification schemes via a network of links constructed by a fast and fully automated mapping approach originally developed for document classification. The web interface enables queries to be made using sequence identifiers, gene symbols, protein functions or amino acid and nucleotide sequences. For the latter query type BLAST similarity search and QuickMatch identity search services have been incorporated, for finding sequences similar (or identical) to a query sequence. ProGMap is meant to help users of high throughput methodologies who deal with partially annotated genomic data.


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