Enhanced protein domain discovery using taxonomy.

ABSTRACT:

Background

It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids.

Results

We show that by incorporating our understanding of the taxonomic distribution of specific protein domains, we can enhance domain recognition in protein sequences. We identify 4447 new instances of Pfam domains in the SP-TREMBL database using this technique, equivalent to the coverage increase given by the last 8.3% of Pfam families and to a 0.7% increase in the number of domain predictions. We use PSI-BLAST to cross-validate our new predictions. We also benchmark our approach using a SCOP test set

SUBMITTER: Coin L 

PROVIDER: S-EPMC434490 | biostudies-literature | 2004 May

REPOSITORIES: biostudies-literature