Several short-read aligners claim that they can perform gapped alignment - I'm new to short-read aligners, and I don't understand what 'gapped alignment' means. How is it different from standard alignment?
Thanks.
Thanks.
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If the organism that you are sequencing has a deletion in comparison with the reference, the gapped aligner will do something like:
Aligners that do not allow for gaps will not be able to map this read.Code:read: ATGAT-ATGATGA ref: ATGATGATGATGA
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What if it is more than one base that is missing, IE:
Will that be aligned as well? What is the maximum of missing bases allowed for it to still be aligned?Code:read: ATGAT----ATGA ref: ATGATGATGATGA
Thanks.Comment
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It will, as long as there is not some other more likely alignment. I would review the Smith-Waterman and Needleman-Wunch sequence comparison algorithms. These algorithms compute actual probability of alignments (well log-odds-ratios) so the following two alignments do not have the same odds:Originally posted by agc View Post
You can see how if you prefer deletions (from the read) over base edits, the former can be preferred (have a better odds ratio). Anyhow, a good intro to bioinformatics book (or course) will clear this up for you.Code:read: ATGAG-A ref: ATGAGGA read: ATGAGA ref: ATGAGG
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