Results 1  10
of
28,761
Local Sequence Alignment FASTA Local Sequence Alignment Against a Database Problem
"... Local Sequence Algignment. The local sequence alignment problem is defined as follows: Given two strings S = s1... sn and T = t1... tm, a substitution matrix Score and an insertion/deletion penalty δ, find a pair of substrings si... si+k of S and tj... tj+l of T that have the best overall alignment ..."
Abstract
 Add to MetaCart
Local Sequence Algignment. The local sequence alignment problem is defined as follows: Given two strings S = s1... sn and T = t1... tm, a substitution matrix Score and an insertion/deletion penalty δ, find a pair of substrings si... si+k of S and tj... tj+l of T that have the best overall
BALSA: Bayesian algorithm for local sequence alignment
 Nucleic Acids Res
, 2002
"... The Smith–Waterman algorithm yields a single alignment, which, albeit optimal, can be strongly affected by the choice of the scoring matrix and the gap penalties. Additionally, the scores obtained are dependent upon the lengths of the aligned sequences, requiring a postanalysis conversion. To overc ..."
Abstract

Cited by 14 (2 self)
 Add to MetaCart
. To overcome some of these shortcomings, we developed a Bayesian algorithm for local sequence alignment (BALSA), that takes into account the uncertainty associated with all unknown variables by incorporating in its forward sums a series of scoring matrices, gap parameters and all possible alignments
Approximate pvalues for local sequence alignments
 Ann. Statist
, 2000
"... Siegmund and Yakir (2000) have given an approximate pvalue when two independent, identically distributed sequences from a nite alphabet are optimally aligned based on a scoring system that rewards similarities according to a general scoring matrix and penalizes gaps (insertions and deletions). The ..."
Abstract

Cited by 39 (1 self)
 Add to MetaCart
Siegmund and Yakir (2000) have given an approximate pvalue when two independent, identically distributed sequences from a nite alphabet are optimally aligned based on a scoring system that rewards similarities according to a general scoring matrix and penalizes gaps (insertions and deletions
Rapid Significance Estimation in Local Sequence Alignment with Gaps
, 2001
"... In order to assess the significance of sequence alignments it is crucial to know the distribution of alignment scores of pairs of random sequences. For gapped local alignment it is empirically known that the shape of this distribution is of the Gumbel form. However, the determination of the paramete ..."
Abstract

Cited by 24 (1 self)
 Add to MetaCart
In order to assess the significance of sequence alignments it is crucial to know the distribution of alignment scores of pairs of random sequences. For gapped local alignment it is empirically known that the shape of this distribution is of the Gumbel form. However, the determination
Measuring Global Credibility with Application to Local Sequence Alignment
"... Computational biology is replete with highdimensional (highD) discrete prediction and inference problems, including sequence alignment, RNA structure prediction, phylogenetic inference, motif finding, prediction of pathways, and model selection problems in statistical genetics. Even though predict ..."
Abstract

Cited by 11 (0 self)
 Add to MetaCart
Computational biology is replete with highdimensional (highD) discrete prediction and inference problems, including sequence alignment, RNA structure prediction, phylogenetic inference, motif finding, prediction of pathways, and model selection problems in statistical genetics. Even though
InDepth Assessment of Local Sequence Alignment
"... Abstract. The overall procedure of searching local similarities among amino acid sequences using local alignment tool has been described in detail. Different phases of the alignment and use of available scoring matrices are explained. The update of scoring matrices based on new sequence information ..."
Abstract
 Add to MetaCart
Abstract. The overall procedure of searching local similarities among amino acid sequences using local alignment tool has been described in detail. Different phases of the alignment and use of available scoring matrices are explained. The update of scoring matrices based on new sequence
Local sequence alignment for an associative model of parallel computation
"... The goal of of sequence alignment is is to to find similarity between the different strings of of genetic information. similar characters � � similar structure ..."
Abstract
 Add to MetaCart
The goal of of sequence alignment is is to to find similarity between the different strings of of genetic information. similar characters � � similar structure
A Local Sequence Alignment Algorithm Using an Associative Model
 of Parallel Computation”, IASTED Computational and Systems Biology (CASB
, 2006
"... Local sequence alignment is widely used to discover structural and hence, functional similarities between biological sequences. While the faster heuristic methods like BLAST and FASTA are useful to compare a single sequence to hundreds or even thousands of sequences in genetic databases such as GenB ..."
Abstract

Cited by 5 (2 self)
 Add to MetaCart
Local sequence alignment is widely used to discover structural and hence, functional similarities between biological sequences. While the faster heuristic methods like BLAST and FASTA are useful to compare a single sequence to hundreds or even thousands of sequences in genetic databases such as Gen
New Approximate Pvalue of Gapped Local Sequence Alignments
"... Received *****; accepted after revision +++++ Presented by £££££ We propose a new method to approximate the significativity of gapped local sequence alignments. We focus on short sequences for which standard methods are known to be less accurate since they have been developed under asymptotics. Our ..."
Abstract
 Add to MetaCart
Received *****; accepted after revision +++++ Presented by £££££ We propose a new method to approximate the significativity of gapped local sequence alignments. We focus on short sequences for which standard methods are known to be less accurate since they have been developed under asymptotics. Our
Accurate Statistics for Local Sequence Alignment with PositionDependent Scoring by RareEvent Sampling
"... Abstract Statistics of pairwise local sequence alignment ("how probable is it to observe a certain alignment score on two random sequences of given length?") mainly focuses on the (mathematically ..."
Abstract
 Add to MetaCart
Abstract Statistics of pairwise local sequence alignment ("how probable is it to observe a certain alignment score on two random sequences of given length?") mainly focuses on the (mathematically
Results 1  10
of
28,761