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PAM sites? I am working on a genome assembly now and I want to try to identify potential g-rna sites around genic regions. This post is pretty helpful.
by daemonk 11y ago
PAM sites? I am working on a genome assembly now and I want to try to identify potential g-rna sites around genic regions. This post is pretty helpful.
- vineetg 11y agoI left PAM sites out of the blog post (it's actually mentioned briefly in the footnotes), as it made the problem slightly more complicated. The final algorithm actually keeps track of the last 20 bases + PAM length, and checks both the edit distance and PAM before deciding if something is a match. The Benchling CRISPR tool will do this for you :)
- daemonk 11y agoCouldn't you use one of the available short read aligners (BWA,bowtie...) available for this also? Most of the aligners use some kind of FM-index for indexing the genome.
- vineetg 11y agoWe messed around with bowtie - it seems like most of these are optimized for the number of alignments being small (i.e. close to 1). Unfortunately, the number of matches for a 20 base guide on the human genome is closer to 1000.