An algorithm for locating non-overlapping regions of maximum alignment score

2005 ◽  
pp. 74-86 ◽  
Author(s):  
Sampath K. Kannan ◽  
Eugene. W. Myers
Keyword(s):  
Alignment Score

scholarly journals Convergent Island Statistics: a fast method for determining local alignment score significance

2005 ◽  
Vol 21 (12) ◽  
pp. 2827-2831 ◽  
Author(s):  
A. Poleksic ◽  
J. F. Danzer ◽  
K. Hambly ◽  
D. A. Debe
Keyword(s):  
Alignment Score ◽  
Local Alignment ◽  
Fast Method

An Algorithm for Locating Nonoverlapping Regions of Maximum Alignment Score

1996 ◽  
Vol 25 (3) ◽  
pp. 648-662 ◽  
Author(s):  
Sampath K. Kannan ◽  
Eugene W. Myers
Keyword(s):  
Alignment Score

scholarly journals Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics

2007 ◽  
Vol 14 (5) ◽  
pp. 655-668 ◽  
Author(s):  
Philipp W. Messer ◽  
Ralf Bundschuh ◽  
Martin Vingron ◽  
Peter F. Arndt
Keyword(s):  
Long Range ◽  
Sequence Alignment ◽  
Alignment Score ◽  
Long Range Correlations ◽  
Score Statistics

Inequalities for the score constant in matching random sequences

1999 ◽  
Vol 36 (02) ◽  
pp. 601-606
Author(s):  
Yunshyong Chow ◽  
Yu Zhang
Keyword(s):  
Monotone Function ◽  
Alignment Score ◽  
Optimal Alignment ◽  
Sequence Matching ◽  
Matching Problem ◽  
Random Sequences

We consider a sequence matching problem involving the optimal alignment score for contiguous sequences; rewarding matches and penalizing for deletions and mismatches. Arratia and Waterman conjectured in [1] that the score constant a(μ, δ) is a strictly monotone function (i) in δ for all positive δ and (ii) in μ if 0 ≤ μ ≤ 2δ. Here we prove that (i) is true for all δ and (ii) is true for some μ.

scholarly journals New finite-size correction for local alignment score distributions

2012 ◽  
Vol 5 (1) ◽  
pp. 286 ◽  
Author(s):  
Yonil Park ◽  
Sergey Sheetlin ◽  
Ning Ma ◽  
Thomas L Madden ◽  
John L Spouge
Keyword(s):  
Finite Size ◽  
Alignment Score ◽  
Local Alignment ◽  
Size Correction ◽  
Finite Size Correction ◽  
Score Distributions

scholarly journals FORGe: prioritizing variants for graph genomes

2018 ◽  
Author(s):  
Jacob Pritt ◽  
Nae-Chyun Chen ◽  
Ben Langmead
Keyword(s):  
Genetic Variants ◽  
Reference Genome ◽  
Software Tool ◽  
Alignment Score ◽  
Alignment Accuracy ◽  
Computational Overhead ◽  
Trade Offs ◽  
The Cost ◽  
Positive Effect ◽  
Allelic Bias

AbstractThere is growing interest in using genetic variants to augment the reference genome into a “graph genome” to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment-score penalty, it also increases both the ambiguity of the reference genome and the cost of storing and querying the genome index. We introduce methods and a software tool called FORGe for modeling these effects and prioritizing variants accordingly. We show that FORGe enables a range of advantageous and measurable trade-offs between accuracy and computational overhead.

scholarly journals Where Does the Alignment Score Distribution Shape Come from?

2010 ◽  
Vol 6 ◽  
pp. EBO.S5875 ◽  
Author(s):  
Philippe Ortet ◽  
Olivier Bastien
Keyword(s):  
Alignment Score ◽  
Score Distribution ◽  
Distribution Shape

Where did the BLOSUM62 alignment score matrix come from?

2004 ◽  
Vol 22 (8) ◽  
pp. 1035-1036 ◽  
Author(s):  
Sean R Eddy
Keyword(s):  
Alignment Score ◽  
Score Matrix
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