[Genome] G-U pair: a match or a mismatch?

[Hiram Clawson]

Good Afternoon Viviana:

The BLAT alignment will consider a G-U pair as a mismatch.

This is not an exact answer, but it may be of some help.
If you would like the alignment to consider a U as a match to the G,
take your query sequence and convert all the U's to G's before submission
to BLAT.  Or were you expecting the U's to also have the ability to
match to T's in the target, and thus match either G or T ?  In that
case you could convert your U's to N's which will then match anything.

--Hiram

Viviana Piccolo wrote:
> Hi!
> I would like to know if the BLAT alignment considers the G-U pair a mismatch or a match and if there are parameters I can use in order to consider the G-U pair as a match.
> Thanks a lot.
> Regards.
> Viviana