Journal of Parallel and Distributed Computing
A batch algorithm for maintaining a topological order
ACSC '10 Proceedings of the Thirty-Third Australasian Conferenc on Computer Science - Volume 102
Fast mapping and precise alignment of AB SOLiD color reads to reference DNA
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: We introduce a novel approach to multiple alignment that is based on an algorithm for rapidly checking whether single matches are consistent with a partial multiple alignment. This leads to a sequence annealing algorithm, which is an incremental method for building multiple sequence alignments one match at a time. Our approach improves significantly on the standard progressive alignment approach to multiple alignment. Results: The sequence annealing algorithm performs well on benchmark test sets of protein sequences. It is not only sensitive, but also specific, drastically reducing the number of incorrectly aligned residues in comparison to other programs. The method allows for adjustment of the sensitivity/specificity tradeoff and can be used to reliably identify homologous regions among protein sequences. Availability: An implementation of the sequence annealing algorithm is available at http://bio.math.berkeley.edu/amap/ Contact: sariel@cs.berkeley.edu