Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP
Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP
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DOI：
10.1093/bioinformatics/btf881
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发表时间：
2003-02-12
期刊：
影响因子：
5.8
通讯作者：
Edwards, D
中科院分区：
文献类型：
--
作者：
Barker, G;Batley, J;Edwards, D
AutoSNP是一种在表达序列标签（EST）数据中检测单核苷酸多态性（snp）和插入/删除多态性（indels）的程序。该程序使用d2cluster和cap3对EST序列进行聚类和对齐，并使用冗余来区分候选snp和序列错误。候选多态性被识别为出现在比对中的多个读取中。对于每个候选SNP，计算两个置信度，即SNP位点多态性的冗余度和候选SNP与比对中其他SNP的共分离度。
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.