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  • Mapping reagents to the genome
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E-RNAi uses Bowtie and/or BLAT to locate designed reagents in the organisms genome sequence (chromosomes or contigs). Besides a very fast mapping of RNAi reagents offered by both programs, BLAT additionally allows for gapped alignments on the genome, which is important to locate sequences that were designed e.g. on CDS sources (spanning exon-exon boundaries).

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