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BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm.

Loving J, Hernandez Y, Benson G - Bioinformatics (2014)

Bottom Line: Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice.We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment.In timed tests, we show that BitPAl runs 7-25 times faster than a standard iterative algorithm.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Biocomputing and Informatics, Graduate Program in Bioinformatics, and Department of Computer Science, Boston University, Boston, MA 02215, USA Laboratory for Biocomputing and Informatics, Graduate Program in Bioinformatics, and Department of Computer Science, Boston University, Boston, MA 02215, USA.

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The ΔV Function Table for the weights  Note that ; ; ; . The ΔH Function Table is the transpose of this table, i.e. the labels ΔH and ΔV are swapped
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btu507-F3: The ΔV Function Table for the weights Note that ; ; ; . The ΔH Function Table is the transpose of this table, i.e. the labels ΔH and ΔV are swapped

Mentions: For the illustrations in this article, we use the scoring weights:M=2,I=−3,G=−5,which yieldmin=−5,max=7, mid=2,low∈{−5,…,2},high∈{3,…,7}.The ΔV Function Table for these weights is shown in Figure 3.Fig. 3.


BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm.

Loving J, Hernandez Y, Benson G - Bioinformatics (2014)

The ΔV Function Table for the weights  Note that ; ; ; . The ΔH Function Table is the transpose of this table, i.e. the labels ΔH and ΔV are swapped
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4221118&req=5

btu507-F3: The ΔV Function Table for the weights Note that ; ; ; . The ΔH Function Table is the transpose of this table, i.e. the labels ΔH and ΔV are swapped
Mentions: For the illustrations in this article, we use the scoring weights:M=2,I=−3,G=−5,which yieldmin=−5,max=7, mid=2,low∈{−5,…,2},high∈{3,…,7}.The ΔV Function Table for these weights is shown in Figure 3.Fig. 3.

Bottom Line: Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice.We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment.In timed tests, we show that BitPAl runs 7-25 times faster than a standard iterative algorithm.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Biocomputing and Informatics, Graduate Program in Bioinformatics, and Department of Computer Science, Boston University, Boston, MA 02215, USA Laboratory for Biocomputing and Informatics, Graduate Program in Bioinformatics, and Department of Computer Science, Boston University, Boston, MA 02215, USA.

Show MeSH
Related in: MedlinePlus