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Bioinformatics Advance Access published online on February 23, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn052
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The effect of sequence quality on sequence alignment

Ketil Malde

Institute of Marine Research, Bergen, Norway

To whom correspondence should be addressed.Dr. Ketil Malde, E-mail: ketil.malde{at}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 paper 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.

Contact: ketil.malde{at}imr.no

Associate Editor: Dr.Limsoon Wong

Received on September 13, 2007; revised on February 1, 2008; accepted on February 1, 2008

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