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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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Code for Zones B, C and D
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btu507-F7: Code for Zones B, C and D

Mentions: Steps 3A and 3B. (Fig. 7). At this point, all the input values for Zone B have been computed (they are the outputs from Zone A), remaining output values are all . The operations are: (i) the AND of appropriate pairs, which intersect along a common diagonal (Zone B); (ii) the AND of the appropriate ΔH vector and all positions without a output (Zone C); (iii) an OR combination of the preceding two results and (iv) a shift of the locations one position to the right for subsequent calculations.Fig. 7.


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

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

Code for Zones B, C and D
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

btu507-F7: Code for Zones B, C and D
Mentions: Steps 3A and 3B. (Fig. 7). At this point, all the input values for Zone B have been computed (they are the outputs from Zone A), remaining output values are all . The operations are: (i) the AND of appropriate pairs, which intersect along a common diagonal (Zone B); (ii) the AND of the appropriate ΔH vector and all positions without a output (Zone C); (iii) an OR combination of the preceding two results and (iv) a shift of the locations one position to the right for subsequent calculations.Fig. 7.

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