Contribution to Bioinformatics search algorithms.

Abstract

hort tandem repeats and homorepeats are considered as low complexity regions (LCRs) which have special properties that are very differen tfro mthos eo fglobula rproteins .Th erule stha tdefi neseconda rystructure elements do not apply when the distribution of amino acids becomes biased. While there is a tendency towards structural disorder in LCRs, various examples, and particularly homorepeats of single amino acids, suggest that very short repeats could adopt structures very difficu lt topredict. For these reasons, we have developed an algorithm to quickly analyze local repeatability along protein sequences, that is, how close a protein fragment is from a perfect repeat. Our method (REpeatability Scanner, RES, accessible at http://cbdm-01.zdv.uni-mainz.de/~munoz/res/) allows to fin dregion swit happroximat eshor trepeat si nprotei nsequences ,an dhelp st ocharacteriz eth evariable use of LCRs and compositional bias.