Method and system for computationally identifying clusters withi

Details Method and system for computationally identifying clusters withi Method and system for computationally identifying clusters withi

Filed on

1998-04-21

Date issued

2000-08-29

Examiner

Horlick, Kenneth R.

Patent Class

Boots, shoes, and leggings

Other Related Categories

435 6, 364497, 364578, 702127, 702 30, G01N 100, G01N 3100, C12Q 168, G06G 748

Type

Patent

Status

active

Patent number

061097764

Description

ABSTRACT:
A method and system for computationally analyzing an initial set of patterns in order to identify subsets of patterns, called clusters, that contain common sub-patterns. The patterns of the initial set of patterns are represented as linear sequences of subunits, and the common sub-patterns occur as sub-sequences of subunits within the linear sequences starting at different positions within the different linear sequences. Variations in the offset and in the sequence of subunits within a common sub-pattern are considered in the analysis. In one embodiment, an initial set of oligonucleotide sequences that are produced by various biochemical techniques are computationally analyzed to identify clusters that may correspond to a number of different binding sites for DNA-binding proteins within one or more double-stranded DNA duplexes. The method places each oligonucleotide sequence within a new cluster and calculates an initial information weight matrix for that cluster. Then, other sequences from the initial set of sequences are added to the cluster and the information weight matrix of the cluster is re-computed until the information content of the information weight matrix falls below a threshold value.

REFERENCES:
patent: 5867402 (1999-02-01), Schneider et al.
Schneider et al NAR vol. 18 No. 20 pp.6097-6100, 1990.
Mehldau et al CABIOS vol. 9, No. 3 pp. 299-314, 1993.
Pesole et al NAR vol. 20, No. 11 pp. 2871-2875, 1992.
Lefevre et al CABIOS vol. 9, No. 3 pp. 349-354, 1993.
Staden NAR vol. 12, No. 1 pp. 505-519, 1984.

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