[EMBOSS] can vectorstrip deal with indels?

[Peter Rice]

Marcus Claesson wrote:
> Hi,
> 
> According to the docs of vectorstrip it has a mismatch parameter which sets
> the max allowed mismatch as a percentage. However, my input sequences
> sometimes contain not just a mismatched character, but also a nucleotide
> insertion/deletion. It seems like vectorstrip can't handle this. Is this
> correct or is there a way to introduce indels as well?

Vectorstrip uses the EMBOSS pattern matching routines. These support
mismatches but not indels.

One possibility is to modify vectorstrip to define all possible indels
in the linker sequences. We can look into the performance impact.

Thanks for the sugestion

Peter Rice