J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading.

Tópicos

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Resumo

The development of automatic approaches for the comparison of protein sequences has become increasingly important. Methods that compare profiles allow for the use of information about whole protein families, resulting in more sensitive and accurate detection of distantly related sequences. In this contribution, we describe a thorough optimization and tests of a profile-to-profile alignment method. A number of different scoring schemes has been implemented and compared on the basis of their ability to identify a template protein from the same SCOP family as a query. In addition to sequence profiles, secondary structure profiles were used to increase the rate of successful detection. Our results show that a properly tuned one-dimensional threading method can recognize a correct template from the same SCOP family nearly as well as structural alignment. Our benchmark set, which might be useful in other similar studies, as well as the fold-recognition software we developed may be downloaded (www.bioshell.pl/profile-alignments).

Resumo Limpo

develop automat approach comparison protein sequenc becom increas import method compar profil allow use inform whole protein famili result sensit accur detect distant relat sequenc contribut describ thorough optim test profiletoprofil align method number differ score scheme implement compar basi abil identifi templat protein scop famili queri addit sequenc profil secondari structur profil use increas rate success detect result show proper tune onedimension thread method can recogn correct templat scop famili near well structur align benchmark set might use similar studi well foldrecognit softwar develop may download wwwbioshellplprofilealign

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