Method for identifying sub-sequences of interest in a sequence

• US 8,046,173 B2
• Filed: 03/06/2008
• Issued: 10/25/2011
• Est. Priority Date: 06/02/2004
• Status: Active Grant

• Current Assignee: Global Life Sciences Solutions Operations UK Ltd. (Danaher Corporation)
• Original Assignee: General Electric Company
• Inventors: Torres, Andrew Soliz, Evans, Scott Charles, Bush, Stephen Francis
• Primary Examiner(s): Clow; Lori A
• Application Number:
  US12/043,609
• Publication Number:
  US 20080270439A1
• Time in Patent Office: 1,328 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

The present technique provides for the analysis of a data series to identify sequences of interest within the series. The analysis may be used to iteratively update a grammar used to analyze the data series or updated versions of the data series. Furthermore, the technique provides for the calculation of a minimum description length heuristic, such as a symbol compression ratio, for each sub-sequence of the analyzed data sequence. The technique may then compare a selected heuristic value against one or more reference conditions to determine if additional iteration is to be performed. The grammar and the data sequence may be updated between iterations to include a symbol representing a string corresponding to the selected heuristic value based upon a non-termination result of the comparison. Alternatively, the string corresponding to the selected heuristic value may be identified as a sequence of interest based upon a termination result of the comparison.

Claims

1. A tangible, machine-readable media, comprising:

code adapted to analyze a data sequence, consisting essentially of a plurality of symbols, based on a grammar comprising at least an initial grammar, wherein the grammar defines at least the plurality of symbols contained within the data sequence;

code adapted to partition the data sequence into a plurality of sub-sequences and to calculate a statistical heuristic for each sub-sequence of the analyzed data sequence;

code adapted to compare a selected statistical heuristic of a selected sub-sequence with one or more reference conditions, and to yield a termination result if the selected statistical heuristic is beyond a threshold defined by the one or more reference conditions or a non-termination result otherwise;

code adapted to update the grammar and the data series with a symbol representing the selected sub-sequence based upon the non-termination result of the comparison; and

code adapted to identify the selected sub-sequence as a sequence of interest based upon the termination result of the comparison.

2. The tangible medium, as recited in claim 1, comprising code adapted to iterate the steps of analyzing, calculating, comparing, and updating until the termination result of the comparison occurs.

3. The tangible medium, as recited in claim 1, wherein the code adapted to calculate the statistical heuristic for each sub-sequence computes the statistical heuristic using a minimum sufficient statistics algorithm.

4. The tangible medium, as recited in claim 1, wherein the code adapted to calculate the statistical heuristic for each sub-sequence computes a symbol compression ratio using an optimal symbol compression ratio algorithm.

5. The tangible medium, as recited in claim 1, wherein the statistical heuristic comprises a minimum description length heuristic and wherein the selected statistical heuristic comprises the minimum description length heuristic having the lowest value.

6. The tangible medium, as recited in claim 1, wherein the statistical heuristic comprises a symbol compression ratio and wherein the selected statistical heuristic comprises the symbol compression ratio having the lowest value.

7. A tangible, machine-readable media, comprising:

code adapted to analyze a biological polymer sequence, consisting essentially of a plurality of symbols, based on a grammar comprising at least an initial grammar, wherein the grammar defines at least the plurality of symbols contained within the biological polymer sequence;

code adapted to partition the biological polymer sequence into a plurality of sub-sequences and to calculate a minimum description length heuristic for each sub-sequence of the analyzed biological polymer sequence;

code adapted to compare a selected minimum description length heuristic corresponding to a selected sub-sequence with one or more reference conditions, and to yield a termination result if the selected minimum description length heuristic is beyond a threshold defined by the one or more reference conditions or a non-termination result otherwise;

code adapted to update the grammar and the biological polymer sequence with a symbol representing the selected sub-sequence based upon the non-termination result of the comparison; and

code adapted to identify the selected sub-sequence as a biological sequence of interest based upon the termination result of the comparison.

8. The tangible medium, as recited in claim 7, comprising:

code adapted to iterate the steps of analyzing, calculating, comparing, and updating until the termination result of the comparison occurs.

9. The tangible medium, as recited in claim 7, wherein the minimum description length heuristic comprises a symbol compression ratio and the selected minimum description length heuristic comprises the symbol compression ratio having the lowest value.