SNPServer: a real-time SNP discovery tool.
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.
Plant Biotechnology Centre, La Trobe University, Bundoora 3086, Victoria, Australia.
David
D
Savage
Jacqueline
J
Batley
Tim
T
Erwin
Erica
E
Logan
Christopher G
CG
Love
Geraldine A C
GA
Lim
Emmanuel
E
Mongin
Gary
G
Barker
German C
GC
Spangenberg
David
D
Edwards
D020407:Internet; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013997:Time Factors; D014584:User-Computer Interface