Automatic extraction of reliable regions from multiple sequence alignments
نویسندگان
چکیده
منابع مشابه
Predicting reliable regions in protein sequence alignments
MOTIVATION Protein sequence alignments have a myriad of applications in bioinformatics, including secondary and tertiary structure prediction, homology modeling, and phylogeny. Unfortunately, all alignment methods make mistakes, and mistakes in alignments often yield mistakes in their application. Thus, a method to identify and remove suspect alignment positions could benefit many areas in prot...
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The Server for Quick Alignment Reliability Evaluation (SQUARE) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three...
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Multiple Sequence alignments are a critical step in phylogeny inference. There is a lack of an appropriate approach which is capable of 1) finding the best global alignment and 2) automating and reproducing manual editing. Progressive alignment is an effective method for multiple Sequence alignments. However, its application in practice has also long been largely hampered because the alignment ...
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Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conse...
متن کاملSeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple al...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2007
ISSN: 1471-2105
DOI: 10.1186/1471-2105-8-s5-s9