RISCI (Repeat Induced Sequence Changes Identifier) is a comprehensive, comparative genomics based, in silico subtractive hybridization tool, to identify differential insertions and associated subtle sequence changes like target site duplications (TSD), 3’ and 5′ flank transductions, insertion mediated deletions, recombination mediated deletions and polymorphism induced by transposons. Post insertion changes such as recombination mediated deletions and disruptions are also picked up by RISCI. It emulates subtractive hybridization in the sense that, only when the locus in the genomes is differential, does it report the sequence changes associated with the transposon insertion.
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BMC Bioinformatics. 2010 Dec 26;11:609. doi: 10.1186/1471-2105-11-609.
RISCI–Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes.
Singh V1, Mishra RK.