SNPServer: a real-time SNP discovery tool

D Savage; Jacqueline Batley; T Erwin; E Logan; CG Love; GAC Lim; E Mongin; G Barker; GC Spangenberg; D Edwards

doi:10.1093/nar/gki462

SNPServer: a real-time SNP discovery tool

D Savage, Jacqueline Batley, T Erwin, E Logan, CG Love, GAC Lim, E Mongin, G Barker, GC Spangenberg, D Edwards

Research output: Contribution to journal › Article › peer-review

45 Citations (Scopus)

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 .

Original language	English
Pages (from-to)	W493-W495
Journal	Nucleic Acids Research
Volume	33
DOIs	https://doi.org/10.1093/nar/gki462
Publication status	Published - 2005

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title = "SNPServer: a real-time SNP discovery tool",

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 .",

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T1 - SNPServer: a real-time SNP discovery tool

AU - Savage, D

AU - Batley, Jacqueline

AU - Erwin, T

AU - Logan, E

AU - Love, CG

AU - Lim, GAC

AU - Mongin, E

AU - Barker, G

AU - Spangenberg, GC

AU - Edwards, D

PY - 2005

Y1 - 2005

N2 - 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 .

AB - 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 .

U2 - 10.1093/nar/gki462

DO - 10.1093/nar/gki462

M3 - Article

SN - 0305-1048

VL - 33

SP - W493-W495

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -

SNPServer: a real-time SNP discovery tool

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