SVM-dependent pairwise HMM: an application to protein pairwise alignments
نویسندگان
چکیده
منابع مشابه
Stochastic pairwise alignments
MOTIVATION The level of sequence conservation between related nucleic acids or proteins often varies considerably along the sequence. Both regions with high variability (mutational hot-spots) and regions of almost perfect sequence identity may occur in the same pair of molecules. The reliability of an alignment therefore strongly depends on the level of local sequence similarity. Especially in ...
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MOTIVATION The local alignment problem for two sequences requires determining similar regions, one from each sequence, and aligning those regions. For alignments computed by dynamic programming, current approaches for selecting similar regions may have potential flaws. For instance, the criterion of Smith and Waterman can lead to inclusion of an arbitrarily poor internal segment. Other approach...
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The parameters by which alignments are scored can strongly affect sensitivity and specificity of alignment procedures. While appropriate parameter choices are well understood for protein alignments, much less is known for genomic DNA sequences. We describe a straightforward approach to scoring nucleotide substitutions in genomic sequence alignments, especially human-mouse comparisons. Scores ar...
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CSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared usin...
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MOTIVATION Overlapping gene coding sequences (CDSs) are particularly common in viruses but also occur in more complex genomes. Detecting such genes with conventional gene-finding algorithms can be difficult for several reasons. If an overlapping CDS is on the same read-strand as a known CDS, then there may not be a distinct promoter or mRNA. Furthermore, the constraints imposed by double-coding...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2017
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btx391