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Nucleic Acids Research Advance Access published online on September 17, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp698
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

FIGfams: yet another set of protein families

Folker Meyer1,2,*, Ross Overbeek3 and Alex Rodriguez2

1Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, 2Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, USA and 3Fellowship for the Interpretation of Genomes, Burr Ridge 60527, IL, USA

*To whom correspondence should be addressed. Email: folker{at}anl.gov

Received June 8, 2009. Revised August 5, 2009. Accepted August 6, 2009.

We present FIGfams, a new collection of over 100 000 protein families that are the product of manual curation and close strain comparison. Using the Subsystem approach the manual curation is carried out, ensuring a previously unattained degree of throughput and consistency. FIGfams are based on over 950 000 manually annotated proteins and across many hundred Bacteria and Archaea. Associated with each FIGfam is a two-tiered, rapid, accurate decision procedure to determine family membership for new proteins. FIGfams are freely available under an open source license. These can be downloaded at ftp://ftp.theseed.org/FIGfams/. The web site for FIGfams is http://www.theseed.org/wiki/FIGfams/


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