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

被引：103

作者：

Barker, G

Batley, J

O'Sullivan, H

Edwards, KJ

Edwards, D ^{[1
]}

机构：

[1] La Trobe Univ, Agr Victoria Plant Biotechnol Ctr, Bundoora, Vic 3086, Australia

[2] Inst Arable Crop Res, Bristol BS41 9AF, Avon, England

[3] Univ Bristol, Sch Biol Sci, Bristol BS8 1UG, Avon, England

来源：

BIOINFORMATICS | 2003年 / 19卷 / 03期

基金：

英国生物技术与生命科学研究理事会;

关键词：

D O I：

10.1093/bioinformatics/btf881

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：421 / 422

页数：2

共 9 条

[1]

[Anonymous], METHOD ENZYMOL

[2] d2_cluster: A validated method for clustering EST and full-length cDNA sequences [J].