Clustering the annotation space of proteins.docVIP

BMC Bioinformatics BioMedCentral Research article Open Access Clustering the annotation space of proteins Victor Kunin* and Christos A Ouzounis Address: Computational Genomics Group, EMBL-EBI, Cambridge, CB10 1SO, UK Email: Victor Kunin* - kunin@ebi.ac.uk; Christos A Ouzounis - ouzounis@ebi.ac.uk * Corresponding author Published: 09 February 2005 Received: 19 August 2004 Accepted: 09 February 2005 BMC Bioinformatics 2005, 6:24 doi:10.1186/1471-2105-6-24 This article is available from: /1471-2105/6/24 ? 2005 Kunin and Ouzounis; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas. Results: Here we report a new approach, named CLAN, which clusters proteins according to both annotation and sequence similarity. This approach is extremely fast, clustering the complete SwissProt database within minutes. It is also accurate, recovering consistent protein families agreeing on average in more than 97% with sequence-based protein families from Pfam. Discrepancies between sequence- and annotation-based clusters were scrutinized and the reasons reported. We demonstrate examples for each of these cases, and thoroughly discuss an example of a propagated error in SwissProt: a vacuolar ATPase subunit M9.2 erroneously annotated as vacuolar ATP synthase subunit H. CLAN algorithm is available from the authors and the CLAN database is accessible at http://maine.ebi.ac.uk:8000/cgi-bin/clan/ClanSearch.pl Conclusions: CLAN creates refined function-and-sequence specific protein families that can be used