Empirical determination of effective gap penalties for sequence comparison
نویسندگان
چکیده
منابع مشابه
Empirical determination of effective gap penalties for sequence comparison
MOTIVATION No general theory guides the selection of gap penalties for local sequence alignment. We empirically determined the most effective gap penalties for protein sequence similarity searches with substitution matrices over a range of target evolutionary distances from 20 to 200 Point Accepted Mutations (PAMs). RESULTS We embedded real and simulated homologs of protein sequences into a d...
متن کاملLocal sequence alignments with monotonic gap penalties
MOTIVATION Sequence alignments obtained using affine gap penalties are not always biologically correct, because the insertion of long gaps is over-penalised. There is a need for an efficient algorithm which can find local alignments using non-linear gap penalties. RESULTS A dynamic programming algorithm is described which computes optimal local sequence alignments for arbitrary, monotonically...
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چکیده ندارد.
15 صفحه اولEffects of Gap Open and Gap Extension Penalties
Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching...
متن کاملExploring the Effects of Gap-Penalties in Sequence-Alignment Approach to Polymorphic Virus Detection
Antiviral software systems (AVSs) have problems in identifying polymorphic variants of viruses without explicit signatures for such variants. Alignment-based techniques from bioinformatics may provide a novel way to generate signatures from consensuses found in polymorphic variant code. We demonstrate how multiple sequence alignment supplemented with gap penalties leads to viral code signatures...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2002
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/18.11.1500