Literature DB >> 12584131

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

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

Abstract

UNLABELLED: 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.

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Year:  2003        PMID： 12584131     DOI： 10.1093/bioinformatics/btf881

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  51 in total

1.  Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.

Authors:  Bastien Chevreux; Thomas Pfisterer; Bernd Drescher; Albert J Driesel; Werner E G Müller; Thomas Wetter; Sándor Suhai
Journal:  Genome Res       Date:  2004-05-12       Impact factor: 9.043

2.  Consensus mapping of major resistance genes and independent QTL for quantitative resistance to sunflower downy mildew.

Authors:  Patrick Vincourt; Falah As-Sadi; Amandine Bordat; Nicolas B Langlade; Jerome Gouzy; Nicolas Pouilly; Yannick Lippi; Frédéric Serre; Laurence Godiard; Denis Tourvieille de Labrouhe; Felicity Vear
Journal:  Theor Appl Genet       Date:  2012-05-11       Impact factor: 5.699

3.  Gene mapping in the wild with SNPs: guidelines and future directions.

Authors:  Jon Slate; Jake Gratten; Dario Beraldi; Jessica Stapley; Matt Hale; Josephine M Pemberton
Journal:  Genetica       Date:  2008-09-09       Impact factor: 1.082

4.  TreeVector: scalable, interactive, phylogenetic trees for the web.

Authors:  Ralph Pethica; Gary Barker; Tim Kovacs; Julian Gough
Journal:  PLoS One       Date:  2010-01-28       Impact factor: 3.240

5.  In silico identification of new genetic variations as potential risk factors for Alzheimer's disease in a microarray-oriented simulation.

Authors:  R R Lemos; C H Castelletti; J L Lima Filho; E T Marques; J R M Oliveira
Journal:  J Mol Neurosci       Date:  2009-03-17       Impact factor: 3.444

6.  Identification of single nucleotide polymorphism in ginger using expressed sequence tags.

Authors:  Arumugam Chandrasekar; Aikkal Riju; Kandiyl Sithara; Sahadevan Anoop; Santhosh J Eapen
Journal:  Bioinformation       Date:  2009-09-30

7.  A pipeline for high throughput detection and mapping of SNPs from EST databases.

Authors:  A M Anithakumari; Jifeng Tang; Herman J van Eck; Richard G F Visser; Jack A M Leunissen; Ben Vosman; C Gerard van der Linden
Journal:  Mol Breed       Date:  2010-01-20       Impact factor: 2.589

8.  Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon.

Authors:  Anti Vasemägi; Riho Gross; Daniel Palm; Tiit Paaver; Craig R Primmer
Journal:  BMC Genomics       Date:  2010-03-08       Impact factor: 3.969

9.  k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage.

Authors:  Lauren M Bragg; Glenn Stone
Journal:  Bioinformatics       Date:  2009-07-01       Impact factor: 6.937

10.  Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies.

Authors:  Shaolin Wang; Eric Peatman; Jason Abernathy; Geoff Waldbieser; Erika Lindquist; Paul Richardson; Susan Lucas; Mei Wang; Ping Li; Jyothi Thimmapuram; Lei Liu; Deepika Vullaganti; Huseyin Kucuktas; Christopher Murdock; Brian C Small; Melanie Wilson; Hong Liu; Yanliang Jiang; Yoona Lee; Fei Chen; Jianguo Lu; Wenqi Wang; Peng Xu; Benjaporn Somridhivej; Puttharat Baoprasertkul; Jonas Quilang; Zhenxia Sha; Baolong Bao; Yaping Wang; Qun Wang; Tomokazu Takano; Samiran Nandi; Shikai Liu; Lilian Wong; Ludmilla Kaltenboeck; Sylvie Quiniou; Eva Bengten; Norman Miller; John Trant; Daniel Rokhsar; Zhanjiang Liu
Journal:  Genome Biol       Date:  2010-01-22       Impact factor: 13.583
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