SNPs

SNP Discovery using AutoSNP

In collaboration with Dave Edwards' group at La Trobe University, we have developed a SNP detection program (AutoSNP) to identify putative polymorphisms between orthologous and parologous sequences from expressed sequence databases. By calculating SNP scores based on redundancy and statistical co segregation of haplotypes, we can differentiate between errors due to sequencing and true genetic polymorphisms. This has advantages in throughput and accuracy over previous methods which relied on the analysis of original sequence trace files. In the latest version the effects of SNPs on the predicted amino acid sequence are displayed, along with the position of conserved protein domains where known.

Data is currently available for wheat barley and maize based on 800K, 400K and 700K ESTs respectively. The SNP reports can be searched by keyword, BLAST will be added soon.

Search cereal SNP data

download the software to build your own SNP reports The program is written in PERL and will run under any unix system.

For further information on this SNP discovery project, please contact Gary Barker

Old SNP data can be found using this link: SNPv1

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Maintained by Gary Barker Last updated Nov 2002