Hit integration for identifying optimal spaced seeds
نویسندگان
چکیده
منابع مشابه
Sensitivity analysis and efficient method for identifying optimal spaced seeds
The novel introduction of spaced seed idea in the filtration stage of sequence comparison by Ma et al. (Bioinformatics 18 (2002) 440) has greatly increased the sensitivity of homology search without compromising the speed of search. Finding the optimal spaced seeds is of great importance both theoretically and in designing better search tool for sequence comparison. In this paper, we study the ...
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Optimal spaced seeds were developed as a method to increase sensitivity of local alignment programs similar to BLASTN. Such seeds have been used before in the program PatternHunter, and have given improved sensitivity and running time relative to BLASTN in genome-genome comparison. We study the problem of computing optimal spaced seeds for detecting homologous coding regions in unannotated geno...
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We study the problem of computing optimal spaced seeds for identifying homologous coding DNA sequences in large genomic data sets. We develop two models of DNA sequence alignment in coding regions, and using data sets from human/Drosophila and human/mouse comparisons, we compute optimal spaced seeds using a dynamic programming algorithm. The seeds we identify are more sensitive by far at identi...
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Filtering is a standard technique for fast approximate string matching in practice. In filtering, a quick first step is used to rule out almost all positions of a text as possible starting positions for a pattern. Typically this step consists of finding the exact matches of small parts of the pattern. In the followup step, a slow method is used to verify or eliminate each remaining position. Th...
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We present improved techniques for finding homologous regions in DNA and protein sequences. Our approach focuses on the core regions of a local pairwise alignment; we suggest new ways to characterize these regions that allow marked improvements in both specificity and sensitivity over existing techniques for sequence alignment. For any such characterization, which we call a vector seed, we give...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2010
ISSN: 1471-2105
DOI: 10.1186/1471-2105-11-s1-s37