SSMAL: similarity searching with alignment graphs.
BACKGROUND
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. Conversely, 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) which utilizes features of the Blast (Altschul et al., J. Mol. Biol., 215, 403-410, 1990) algorithm and part of the Blast code. Our software allows both scanning of 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, an SSMAL scan of a database such as ProDom would be 20-30 times faster that a profile scan. In the worst case, a SSMAL search is approximately 9 times faster than a profile search.


BACKGROUND
http://www.dkfz-heidelberg.de/tbi/ people/nicodeme and follow the hyperlink SSMAL.


BACKGROUND
p.nicodeme@DKFZ-Heidelberg.de
Nicodème
P
P
INRIA-Rocquencourt and LIX Ecole Polytechnique, France; Present address: DKFZ, Abt. Theoretische Bioinformatik, INF 280, D-69120 Heidelberg, Germany. p.nicodeme@DKFZ-Heidelberg.de
D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D017124:Conserved Sequence; D016208:Databases, Factual; D005914:Globins / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software
D011506:Proteins; D005914:Globins