SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development.
With the influx of various SNP genotyping assays in recent years, there has been a need for an assay that is robust, yet cost effective, and could be performed using standard gel-based procedures. In this context, CAPS markers have been shown to meet these criteria. However, converting SNPs to CAPS markers can be a difficult process if done manually. In order to address this problem, we describe a computer program, SNP2CAPS, that facilitates the computational conversion of SNP markers into CAPS markers. 413 multiple aligned sequences derived from barley ESTs were analysed for the presence of polymorphisms in 235 distinct restriction sites. 282 (90%) of 314 alignments that contain sequence variation due to SNPs and InDels revealed at least one polymorphic restriction site. After reducing the number of restriction enzymes from 235 to 10, 31% of the polymorphic sites could still be detected. In order to demonstrate the usefulness of this tool for marker development, we experimentally validated some of the results predicted by SNP2CAPS.
Thiel
Thomas
T
Institute for Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany.
Kota
Raja
R
Grosse
Ivo
I
Stein
Nils
N
Graner
Andreas
A
D001483:Base Sequence; D004262:DNA Restriction Enzymes / Q000378:metabolism; D020224:Expressed Sequence Tags; D005819:Genetic Markers / Q000235:genetics*; D005838:Genotype; D001467:Hordeum / Q000235:genetics; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software
D005819:Genetic Markers; D004262:DNA Restriction Enzymes