ReAligner: a program for refining DNA sequence multi-alignments. 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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References in zbMATH (referenced in 2 articles )
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- DeBlasio, Dan; Kececioglu, John: Parameter advising for multiple sequence alignment (2017)
- Chu, Wei-Ta; Chen, Herng-Yow: Toward better retrieval and presentation by exploring cross-media correlations (2005) ioport