System and method for encoding and detecting extensible...

Details System and method for encoding and detecting extensible... System and method for encoding and detecting extensible...

2007-04-10

2007-04-10

Robinson, Greta (Department: 2165)

Data processing: database and file management or data structures

Database design

Data structure types

C707S793000

Reexamination Certificate

active

10677016

ABSTRACT:
Given an input sequence of data, a rigid pattern is a repeating sequence, possibly interspersed with don't-care characters. The data can be a sequence of characters or sets of characters or even real values. In practice, the patterns or motifs of interest are the ones that also allow a variable number of gaps (or don't-care characters): these are patterns with spacers termed extensible patterns. In a bioinformatics context, similar patterns have also been called flexible patterns or motifs. A system according to the invention discovers all the maximal extensible motifs in the input. The flexibility is succinctly defined by a single integer parameter D≧1 which is interpreted as the allowable space to be between 1 and D characters between two successive solid characters in a reported motif.

REFERENCES:
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patent: 6373971 (2002-04-01), Floratos et al.
patent: 6571230 (2003-05-01), Parida
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Abhijit Chattaraj and Laxmi Parida, “An Inexact-Suffix Tree Based Algorithm for Detecting Extensible Patterns.”

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