Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
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.
Brusca John S
IP Genesis, Inc.
Milosavljevic Aleksandar
Skibinsky Anna
LandOfFree
Positional hashing method for performing DNA sequence... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Positional hashing method for performing DNA sequence..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Positional hashing method for performing DNA sequence... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4170190