This work describes the development of a program that predicts whether or not a 
polypeptide sequence from a Gram-negative bacterium is an integral beta-barrel 
outer membrane protein. The program, called the beta-barrel Outer Membrane 
protein Predictor (BOMP), is based on two separate components to recognize 
integral beta-barrel proteins. The first component is a C-terminal pattern 
typical of many integral beta-barrel proteins. The second component calculates 
an integral beta-barrel score of the sequence based on the extent to which the 
sequence contains stretches of amino acids typical of transmembrane 
beta-strands. The precision of the predictions was found to be 80% with a recall 
of 88% when tested on the proteins with SwissProt annotated subcellular 
localization in Escherichia coli K 12 (788 sequences) and Salmonella typhimurium 
(366 sequences). When tested on the predicted proteome of E.coli, BOMP found 103 
of a total of 4346 polypeptide sequences to be possible integral beta-barrel 
proteins. Of these, 36 were found by BLAST to lack similarity (E-value score < 
1e-10) to proteins with annotated subcellular localization in SwissProt. BOMP 
predicted the content of integral beta-barrels per predicted proteome of 10 
different bacteria to range from 1.8 to 3%. BOMP is available at 
http://www.bioinfo.no/tools/bomp.