[EMBOSS] Is vectorstrip gapless by design or is it a bug ?

[pmr at ebi.ac.uk]

Dear Charles,

> In the following example, vectorstrip identifies the first primer with six
> mismatches, although it has only two. It means that if I run vectorstrip
> with
> a -mismatch value lower that 29, I do miss the primer.

vectorstrip is indeed gapless by design. The algorithm is rather crude and
could be updated. I am currently looking into other vectorstrip issues and
now is a good time to ask questions about it.

Being gapless, you have to look at the number of mismatches without
inserting gaps. I believe it was designed with the asusmption that 5'
vector matches would be in good quality sequence.

Other change requests I am looking at are:

an option -allsequences to report all sequences in the output report (so
that web interfaces can more easily parse the output)

checking some test cases for possible missed 3' matches

better annotation in the fasta format sequence output (does anyone use that?)

hope that helps

Peter