Positional hashing method for performing DNA sequence...

Details Positional hashing method for performing DNA sequence... Positional hashing method for performing DNA sequence...

2003-02-26

2010-10-05

Brusca, John S (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C702S022000

Reexamination Certificate

active

07809510

ABSTRACT:
Positional Hashing, a novel method for detecting similarities between texts such as DNA sequences, amino acid sequences, and texts in natural language is disclosed. The method is particularly well suited for large-scale comparisons such as that of mutual comparisons of millions of sequence fragments that result from mammalian-scale sequencing projects and for whole-genome comparisons of multiple mammalian genomes. Positional Hashing is carried out by breaking the sequence comparison problem along its natural structure, solving the subproblems independently, and then collating the solutions into an overall result. The decomposition of the problem into subproblems enables parallelization, whereby a large number of nodes in a computer cluster or a computer farm are concurrently employed on solving the problem without incurring the quadratic time performance penalty characteristic of prior art. Positional Hashing may be used by itself or as a filtering step in conjunction with a variety of sequence comparison algorithms.

REFERENCES:
Buhler, “Efficient large-scale sequence comparison by locality-sensitive hashing,” Bioinformatics, vol. 17 (2001) pp. 419-428.
Ladunga et al., “FAST-SWAP and FASTA-PAT: Pattern Database Searches Using Combinations of Aligned Amino Acids, and a Novel Scoring Theory,” J. Mol. Biol., vol. 259 (1996), pp. 840-854.

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