SNPServer: a real-time SNP discovery tool | Zendy

David A. Savage | Zendy; Jacqueline Batley | Zendy; Tim Erwin | Zendy; Erica Logan | Zendy; Christopher G. Love | Zendy; Geraldine Lim | Zendy; Emmanuel Mongin | Zendy; Gary Barker | Zendy; Germán Spangenberg | Zendy; David Edwards | Zendy

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SNPServer: a real-time SNP discovery tool

Author(s) -

David A. Savage,

Jacqueline Batley,

Tim Erwin,

Erica Logan,

Christopher G. Love,

Geraldine Lim,

Emmanuel Mongin,

Gary Barker,

Germán Spangenberg,

David Edwards

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki462

Subject(s) - biology , snp , indel , single nucleotide polymorphism , genetics , molecular inversion probe , tag snp , computational biology , snp genotyping , genotype , gene

SNPServer is a real-time flexible tool for the discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data. The program uses BLAST, to identify related sequences, and CAP3, to cluster and align these sequences. The alignments are parsed to the SNP discovery software autoSNP, a program that detects SNPs and insertion/deletion polymorphisms (indels). Alternatively, lists of related sequences or pre-assembled sequences may be entered for SNP discovery. SNPServer and autoSNP use redundancy to differentiate between candidate SNPs and sequence errors. 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. SNPServer is available at http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html.

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