ReAligner: a program for refining DNA sequence multi-alignments.

E L Anson; E W Myers

doi:10.1089/cmb.1997.4.369

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ReAligner: a program for refining DNA sequence multi-alignments.

E L Anson·E W Myers

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Abstract

We present a round-robin realignment algorithm that improves a potentially crude initial alignment of an assembled collection of DNA sequence fragments, as might, for example, be output by a typical fragment assembly program. The algorithm uses a weighted combination of two scoring schemes to achieve superior multi-alignments, and employs a banded dynamic programming variation to achieve a running time that is linear in the amount of sequence in the data set. We demonstrate that the algorithm improves upon the alignments produced by other assembly programs in a series of empirical experiments on simulated data. Finally, we present a pair of programs embodying the algorithms that are available from the Web site ftp://ftp.cs.arizona.edu/realigner.

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Algorithms Base Sequence DNA Models, Genetic Molecular Sequence Data Sequence Alignment Software Journal Article

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E L Anson, E W Myers. 1997. ReAligner: a program for refining DNA sequence multi-alignments.. https://doi.org/10.1089/cmb.1997.4.369

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