Hi all, noob MSc here. I want to confirm the knockdown targets of my siRNAs (i.e. check an siRNA knocks down more than one transcript variant)
I’d like to find an efficient method.
Method #1: CTRL+F my siRNA sequence on the FASTA mRNA sequence Con: this only allows for 100% alignment
Method #2: BLAST my siRNA sequence to the whole genome Pro: Allows for similar alignment Con: Too many redundant predicted targets, and unclear which transcript variants are hits
Question: Is there a way to BLAST a short sequence to a defined set of sequences rather than the whole genome? I want to BLAST my siRNA sequence to just the sequence of my variants, nothing else.
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