Ketil Malde1. 1. Institute of Marine Research, Bergen, Norway. ketil.malde@imr.no
Abstract
MOTIVATION: The nucleotide sequencing process produces not only the sequence of nucleotides, but also associated quality values. Quality values provide valuable information, but are primarily used only for trimming sequences and generally ignored in subsequent analyses. RESULTS: This article describes how the scoring schemes of standard alignment algorithms can be modified to take into account quality values to produce improved alignments and statistically more accurate scores. A prototype implementation is also provided, and used to post-process a set of BLAST results. Quality-adjusted alignment is a natural extension of standard alignment methods, and can be implemented with only a small constant factor performance penalty. The method can also be applied to related methods including heuristic search algorithms like BLAST and FASTA. AVAILABILITY: http://malde.org/~ketil/qaa.
MOTIVATION: The nucleotide sequencing process produces not only the sequence of nucleotides, but also associated quality values. Quality values provide valuable information, but are primarily used only for trimming sequences and generally ignored in subsequent analyses. RESULTS: This article describes how the scoring schemes of standard alignment algorithms can be modified to take into account quality values to produce improved alignments and statistically more accurate scores. A prototype implementation is also provided, and used to post-process a set of BLAST results. Quality-adjusted alignment is a natural extension of standard alignment methods, and can be implemented with only a small constant factor performance penalty. The method can also be applied to related methods including heuristic search algorithms like BLAST and FASTA. AVAILABILITY: http://malde.org/~ketil/qaa.
Authors: Rachel Marine; Shawn W Polson; Jacques Ravel; Graham Hatfull; Daniel Russell; Matthew Sullivan; Fraz Syed; Michael Dumas; K Eric Wommack Journal: Appl Environ Microbiol Date: 2011-09-23 Impact factor: 4.792
Authors: Kai Wang; Darshan Singh; Zheng Zeng; Stephen J Coleman; Yan Huang; Gleb L Savich; Xiaping He; Piotr Mieczkowski; Sara A Grimm; Charles M Perou; James N MacLeod; Derek Y Chiang; Jan F Prins; Jinze Liu Journal: Nucleic Acids Res Date: 2010-08-27 Impact factor: 16.971
Authors: Eitan Halper-Stromberg; Jared Steranka; Kathleen H Burns; Sarven Sabunciyan; Rafael A Irizarry Journal: Bioinformatics Date: 2014-02-04 Impact factor: 6.937
Authors: George L Sutphin; J Matthew Mahoney; Keith Sheppard; David O Walton; Ron Korstanje Journal: PLoS Comput Biol Date: 2016-11-03 Impact factor: 4.475
Authors: Bo Yuan; Pengfei Liu; Aditya Gupta; Christine R Beck; Anusha Tejomurtula; Ian M Campbell; Tomasz Gambin; Alexandra D Simmons; Marjorie A Withers; R Alan Harris; Jeffrey Rogers; David C Schwartz; James R Lupski Journal: PLoS Genet Date: 2015-12-07 Impact factor: 5.917