Statistics of local multiple alignments
نویسندگان
چکیده
منابع مشابه
Statistics of local multiple alignments
SUMMARY BLAST statistics have been shown to be extremely useful for searching for significant similarity hits, for amino acid and nucleotide sequences. Although these statistics are well understood for pairwise comparisons, there has been little success developing statistical scores for multiple alignments. In particular, there is no score for multiple alignment that is well founded and treated...
متن کاملSampling rare events: statistics of local sequence alignments.
A method to calculate probability distributions in regions where the events are very unlikely (e.g., p approximately 10(-40)) is presented. The basic idea is to map the underlying model on a physical system. The system is simulated at a low temperature, such that preferably configurations with originally low probabilities are generated. Since the distribution of such a physical system is known,...
متن کاملSuboptimal Local Alignments Across Multiple Scoring Schemes
Sequence alignment algorithms have a long standing tradition in bioinformatics. In this paper, we formulate an extension to existing local alignment algorithms: local alignments across multiple scoring functions. For this purpose, we use the Waterman-Eggert algorithm for suboptimal local alignments as template and introduce two new features therein: 1) an alignment of two strings over a set of ...
متن کاملApproximate Statistics of Gapped Alignments
A heuristic approximation to the score distribution of gapped alignments in the logarithmic domain is presented. The method applies to comparisons between random, unrelated protein sequences, using standard score matrices and arbitrary gap penalties. It is shown that gapped alignment behavior is essentially governed by a single parameter, alpha, depending on the penalty scheme and sequence comp...
متن کاملWhole Genome Alignments Based On Local Alignments
Given the genomes (DNA) of two related species, one of the whole genome alignment tasks is to locate regions on the genomes that possibly contain genes conserved over the two species. Most of the existing whole genome alignment software tools, MUMmer (Delcher et al., 2002; Kurtz et al., 2004), MaxMincluster (Wong et al., 2004), and MSS (Chan et al., 2004), generate Maximal Unique Matches (MUMs)...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2005
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bti1042