Gapped Alignment

[agc]

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.

[Pepe]

If the organism that you are sequencing has a deletion in comparison with the reference, the gapped aligner will do something like:

read: ATGAT-ATGATGA
ref:  ATGATGATGATGA

Aligners that do not allow for gaps will not be able to map this read.

[agc]

What if it is more than one base that is missing, IE:

read: ATGAT----ATGA
ref:  ATGATGATGATGA

Will that be aligned as well? What is the maximum of missing bases allowed for it to still be aligned?

Thanks.

[nilshomer]

What if it is more than one base that is missing, IE:

read: ATGAT----ATGA
ref:  ATGATGATGATGA

Will that be aligned as well? What is the maximum of missing bases allowed for it to still be aligned?

Thanks.

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:

read: ATGAG-A
ref:  ATGAGGA

read: ATGAGA
ref:  ATGAGG

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.