Bioinformatics Vol. 17 no. 3 2001
Pages 249-261
© 2001 Oxford University Press
Original Paper |
MetaFam: a unified classification of protein families. I. Overview and statistics
Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA
Received on May 31, 2000
; revised on July 4, 2000
; accepted on October 12, 2000
Motivation: Protein sequence classification is becoming an
increasingly important means of organizing the voluminous data
produced by large-scale genome sequencing projects. At present,
there are several independent classification methods. To aid the
general classification effort, we have created a unified protein
family resource, MetaFam. MetaFam is a protein family classification
built upon 10 publicly-accessible protein family databases
(Blocks
, DOMO, Pfam, PIR-ALN, PRINTS, PROSITE, ProDom,
PROTOMAP, SBASE, and SYSTERS). MetaFam’s family
‘supersets’, as we call them, are created automatically
using set-theory to compare families among the databases. Families
of one database are matched to those in another when the
intersection of their members exceeds all other possible family
pairings between the two databases. Pairwise family matches are
drawn together transitively to create a new list of protein family
supersets.
Results: MetaFam family supersets have several useful features: (1) each superset contains more members than the families from which it is composed, because each of the component family databases only works with a subset of our full non-redundant set of proteins; (2) conflicting assignments can be pinpointed quickly, since our analysis identifies individual members that are in conflict with the majority consensus; (3) family descriptions that are absent from automated databases can frequently be assigned; (4) statistics have been computed comparing domain boundaries, family size distributions, and overall quality of MetaFam supersets; (5) the supersets have been loaded into a relational database to allow for complex queries and visualization of the connections among families in a superset and the consensus of individual domain members; and (6) the quality of individual supersets has been assessed using numerous quantitative measures such as family consistency, connectedness, and size. We anticipate this new resource will be particularly useful to genomic database curators.
Availability: Free access to the MetaFam web server is provided to all users at http://metafam.ahc.umn.edu/.
Contact: metafam{at}ahc.umn.edu
Supplementary information: Detailed distribution plots on MetaFam 2.0 supersets and its constituent family databases (e.g. superset/family sizes, domain boundary comparisons) are shown at http://metafam.ahc.umn.edu/mf2.0/stats.html. Statistics on the current release of MetaFam can be found at http://metafam.ahc.umn.edu/current_release/stats.html.
* To whom correspondence should be addressed.
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