<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>A method for assigning functions to unknown sequences based on finding correlations between short signals and functional annotations in a protein database is presented.
This approach is based on keyword (KW) and feature (FT) information stored in
the SWISS-PROT database. The former refers to particular protein characteristics
and the latter locates these characteristics at a specific sequence position. In this way,
a certain keyword is only assigned to a sequence if sequence similarity is found in
the position described by the FT field. Exhaustive tests performed over sequences
with homologues (cluster set) and without homologues (singleton set) in the database
show that assigning functions is much ’cleaner’ when information about domains (FT
field) is used, than when only the keywords are used.</p>
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Comp Funct Genomics. 2002 Oct; 3(5):423-440