Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.
Bioinformatics
; 25(1): 6-13, 2009 Jan 01.
Article
in En
| MEDLINE
| ID: mdl-18974170
ABSTRACT
MOTIVATION A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files. RESULTS:
Compared with other aligners, Slider has higher alignment accuracy and efficiency. In addition, given that Slider matches bases with probabilities other than the most probable, it significantly reduces the percentage of base mismatches. The result is that its SNP predictions are more accurate than other SNP prediction approaches used today that start from the most probable sequence, including those using base quality.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Algorithms
/
Probability
/
Sequence Alignment
/
Polymorphism, Single Nucleotide
Type of study:
Diagnostic_studies
/
Prognostic_studies
Limits:
Humans
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2009
Document type:
Article
Affiliation country:
Canada