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Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W493-5.

SNPServer: a real-time SNP discovery tool.

Author information

1
Plant Biotechnology Centre, La Trobe University, Bundoora 3086, Victoria, Australia.

Abstract

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.

PMID:
15980519
PMCID:
PMC1160223
DOI:
10.1093/nar/gki462
[Indexed for MEDLINE]
Free PMC Article

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