TAILIEUCHUNG - Báo cáo sinh học: " AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences. | Guerrero et al. Algorithms for Molecular Biology 2010 5 24 http content 5 1 24 AMR ALGORITHMS FOR MOLECULAR BIOLOGY SOFTWARE ARTICLE Open Access AlignMiner a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences P s f 1 1 2 I- I-X z- . 2 Dario Guerrero Rocío Bautista David P Villalobos Francisco R Cantón M Gonzalo Claros 1 Abstract Background Multiple sequence alignments are used to study gene or protein function phylogenetic relations genome evolution hypotheses and even gene polymorphisms. Virtually without exception all available tools focus on conserved segments or residues. Small divergent regions however are biologically important for specific quantitative polymerase chain reaction genotyping molecular markers and preparation of specific antibodies and yet have received little attention. As a consequence they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences focusing particularly on divergence. It accepts alignments protein or nucleic acid obtained using any of a variety of algorithms which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved divergent regions Entropy being the method that provides the highest number of regions with the greatest length and Weighted being the most restrictive. Conserved divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and inspect their results on a different computer. Data can be downloaded onto a user disk in standard formats. n

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