Title: Method and apparatus for biological sequence comparison

Abstract

A method and apparatus for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greatermore » than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. « less

Inventors:

Marr, Thomas G ^[1]; Chang, William I-Wei ^[1]

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1. Huntington, NY

Issue Date:

Wed Jan 01 00:00:00 EST 1997

Research Org.:

Cold Spring Harbor Lab., NY (United States)

OSTI Identifier:

871286

Patent Number(s):

5701256

Assignee:

Cold Spring Harbor Laboratory (Cold Spring Harbor, NY)

Patent Classifications (CPCs):

G - PHYSICS G06 - COMPUTING G06F - ELECTRIC DIGITAL DATA PROCESSING

G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

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G - PHYSICS G06 - COMPUTING G06F - ELECTRIC DIGITAL DATA PROCESSING

G06F16/90344 - {by using string matching techniques}

G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

G16B30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B30/10 - Sequence alignment

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DOE Contract Number:  

FG02-91ER61190

Resource Type:

Patent

Country of Publication:

United States

Language:

English

Subject:

method; apparatus; biological; sequence; comparison; comparing; sequences; source; subject; query; takes; input; set; target; similarity; levels; evolutionary; distances; units; pam; fragments; similar; level; statistically; significant; device; filters; average; required; compared; remaining; matches; filtering; divides; overlapping; blocks; block; sufficiently; contain; minimum-length; alignment; filter; compares; fragment; determines; match; determined; provide; upper; threshold; values; regions; length; mean; value; unit; score; concatenated; form; union; current; provides; indication; local; determined set; /702/382/