Motivation. We want to provide biologists with a fast and sensitive scanning tool for searching local alignments of a protein query sequence against databases of protein multiple alignments such as ProDom. Reversely, we want to provide a tool for locally aligning a protein multiple alignment query against a protein database such as SWISSPROT.
Results. We developed the program SSMAL (Shuffling Similarities with Multiple Alignments) that utilizes features of the Blast algorithm and part of the Blast code. Our software allows both scanning multiple alignments and searching with a multiple alignment. Deletions in the multiple alignment only are handled and a SSMAL search may miss some similarities found by a profile search. However a SSMAL scan of a database as ProDom would be 20 to 30 times faster that a profile scan. In the worst case a SSMAL search is about 9 times faster that a profile search.