Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP

Gary Barker; Jacqueline Batley; Helen O' Sullivan; Keith J Edwards; David Edwards

doi:10.1093/bioinformatics/btf881

Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP

Bioinformatics. 2003 Feb 12;19(3):421-2. doi: 10.1093/bioinformatics/btf881.

Authors

Gary Barker¹, Jacqueline Batley, Helen O' Sullivan, Keith J Edwards, David Edwards

Affiliation

¹ Institute of Arable Crop Research, Long Ashton, Bristol, BS41 9AF, UK.

PMID: 12584131
DOI: 10.1093/bioinformatics/btf881

Abstract

AutoSNP is a program to detect single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) in expressed sequence tag (EST) data. The program uses d2cluster and cap3 to cluster and align EST sequences, and uses redundancy to differentiate between candidate SNPs and sequence errors. Candidate polymorphisms are identified as occurring in multiple reads within an alignment. For each candidate SNP, two measures of confidence are calculated, the redundancy of the polymorphism at a SNP locus and the co segregation of the candidate SNP with other SNPs in the alignment.

Availability: The program was written in PERL and is freely available to non-commercial users by request from the authors.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't

MeSH terms

Cluster Analysis
Expressed Sequence Tags*
Genetic Markers*
Polymorphism, Single Nucleotide / genetics*
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software
Zea mays / genetics

Substances

Genetic Markers