Find indels between two short sequences

Question

I have two sequences, say AAAGCTCGAGG and AAAGCGAGG. I need a convenient tool which shows me insertions or deletions between these, i.e. in this case something like

AAAGCTCGAGG
|||||  ||||
AAAGC  GAGG
2bp deletion starting at base pair 5

and also insertions such as

AAAGCTC GAGG
||||||| ||||
AAAGCTCTGAGG
1bp insertion at base pair 7

Does something like that exist? Blastn finds the alignment of course, but only outputs the number of gaps, not their position. I guess I could parse a pileup, but do not want to create a bam file from one of the sequences first, so samtools seems to be out. Any further ideas?

Answer 1

Smith-Waterman is guaranteed to give you the best alignment given your choice of substitution matrix. For a few such tiny sequences, it's what I would use. Many implementations exist.

Answer 2

Perhaps you could use something like SearchIO to parse the output of BLAST, to get the desired alignment attributes: https://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-module.html

Answer 3

blastn should be able to output this format of alignment result, using the --outfmt 0 option

Answer 4

Is there any particular reason why you don't want a BAM output format? If the sequences are sufficiently long, then the CIGAR field from the SAM output of minimap2 could be used:

minimap2 -a seq1.fa seq2.fa | samtools view | awk '{print $6}'