BlastDigester--a web-based program for efficient CAPS marker design.

Abstract Single nucleotide polymorphisms (SNPs) and insertion and deletions (InDels), the most common type of intra-specific sequence polymorphism, are rich resources for creating DNA markers for genotyping. In this article, we present a web-based program for generating cleaved amplified polymorphic sequence (CAPS) markers, PCR-based markers that use polymorphism in restriction endonuclease digestion patterns (snip-SNPs). BlastDigester computationally ‘digests' the sequence alignments that are returned in a Blast search, identifies snip-SNPs and simplifies PCR-primer generation through dynamic links to Primer3, a primer design program.

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