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
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