Sampling rare events: Statistics of local sequence alignments
نویسندگان
چکیده
منابع مشابه
Sampling 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 کاملStatistics 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 کاملEnhanced sampling of rare events
We present a method to enhance sampling of a given reaction coordinate by projecting part of the random thermal noise along a preferential direction. The approach is promising to study rough energy landscapes and highly activated barriers that can be overcome by increasing the attempt frequency. Furthermore it allows us to rescale a given reaction coordinate without biasing the configurational ...
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...
متن کاملMaking Sense of Score Statistics for Sequence Alignments
The search for similarity between two biological sequences lies at the core of many applications in bioinformatics. This paper aims to highlight a few of the principles that should be kept in mind when evaluating the statistical significance of alignments between sequences. The extreme value distribution is first introduced, which in most cases describes the distribution of alignment scores bet...
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: Physical Review E
سال: 2002
ISSN: 1063-651X,1095-3787
DOI: 10.1103/physreve.65.056102