QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

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ID: 110531
2006
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Abstract
Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels) in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs) with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans. QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at http://www.bioinformatics.nl/tools/snpweb/ and as Additional files.
Reference Key
tang2006bmcqualitysnp: Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Jifeng Tang;Ben Vosman;Roeland E Voorrips;C Gerard van der Linden;Jack AM Leunissen;Jifeng Tang;Ben Vosman;Roeland E Voorrips;C Gerard van der Linden;Jack AM Leunissen;
Journal BMC Bioinformatics
Year 2006
DOI
doi:10.1186/1471-2105-7-438
URL
http://dx.doi.org/10.1186%2F1471-2105-7-438
Keywords
bioinformatics algorithms microarrays computational biology/bioinformatics computer appl. in life sciences databases National Center for Biotechnology Information NCBI NLM MEDLINE genetic pubmed abstract nih national institutes of health national library of medicine research support non-u.s. gov't Evaluation Study Base Sequence Molecular Sequence Data Polymorphism expressed sequence tags* software* pmid:17029635 pmc1618865 doi:10.1186/1471-2105-7-438 jifeng tang ben vosman jack a m leunissen chromosome mapping / methods* dna mutational analysis / methods* dna transposable elements / genetics* diploidy gene deletion* single nucleotide / genetics* polyploidy

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