Rapid motif-based prediction of circular permutations in multi-domain proteins.
BACKGROUND
Rearrangements of protein domains and motifs such as swaps and circular permutations (CPs) can produce erroneous results in searching sequence databases when using traditional methods based on linear sequence alignments. Circular permutations are also of biological relevance because they can help to better understand both protein evolution and functionality.


RESULTS
We have developed an algorithm, RASPODOM, which is based on the classical recursive alignment scheme. Sequences are represented as strings of domains taken from precompiled resources of domain (motif) databases such as ProDom. The algorithm works several orders of magnitude faster than a reimplementation of the existing CP detection algorithm working on strings of amino acids, produces virtually no false positives and allows the discrimination of true CPs from 'intermediate' CPs (iCPs). Several true CPs which have not been reported in literature so far could be identified from Swiss-Prot/TrEMBL within minutes.
Weiner
January
J
Division of Bioinformatics, School of Biology, Institute of Botany, The Westphalian Wilhelm's University of Münster Schlossplatz 4 D48149 Münster, Germany.
Thomas
Geraint
G
Bornberg-Bauer
Erich
E
D000465:Algorithms; D020816:Amino Acid Motifs; D003198:Computer Simulation; D030562:Databases, Protein; D014644:Genetic Variation; D008956:Models, Chemical; D015233:Models, Statistical; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000032:analysis* / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins