Methods and systems for aligning repetitive dna elements
AssigneeIllumina, Inc.
InventorsJocelyne BRUAND, Tom RICHARDSON, Tobias MANN
Life of this patent
Estimating the term…
Abstract
Presented are methods and systems for aligning repetitive DNA elements. The methods and systems use the conserved flanks of repetitive polymorphic loci to effectively determine the length and sequence of the repetitive DNA element.
Claims26
A method for determining the length of a polymorphic repetitive DNA element having a repeat region situated between a first conserved flanking region and a second conserved flanking region, the method comprising:
- (a) providing a data set comprising at least one sequence read of the polymorphic repetitive DNA element;
- (b) providing a reference sequence comprising the first conserved flanking region and the second conserved flanking region;
- (c) aligning a portion of the first flanking region of the reference sequence to the sequence read;
- (d) aligning a portion of the second flanking region of the reference sequence to the sequence read;
- and
- (e) determining the length and/or sequence of the repeat region;
- wherein at least steps (c), (d) and (e) are performed using a suitably programmed computer.
A system for determining the length of a polymorphic repetitive DNA element having a repeat region situated between a first conserved flanking region and a second conserved flanking region, the system comprising:
- a processor;
- and
- a program for determining the length of a polymorphic repetitive DNA element, the program comprising instructions for:
- (a) providing a data set comprising at least one sequence read of the polymorphic repetitive DNA element;
- (b) providing a reference sequence comprising the first conserved flanking region and the second conserved flanking region;
- (c) aligning a portion of the first flanking region of the reference sequence to the sequence read;
- (d) aligning a portion of the second flanking region of the reference sequence to the sequence read;
- and
- (e) determining the length and/or sequence of the repeat region.
-48. (canceled)
Dependencies are inferred from the claim text.