[Bioperl-l] How to check mRNA moltype?

Mark Wilkinson mwilkinson@gene.pbi.nrc.ca
Wed, 17 Oct 2001 08:10:17 -0600

This could be part of the post-processing of SeqI modules that I am planning to
put some serious effort into starting next month.

I hadn't considered this as a problem (given that a transcript ~= mRNA, with
just a small amount of character translation), but if it is important to some
people there is no reason why the Bio::SemanticFeatureInterpreter::Interface's
couldn't include an option to make "real" mRNA molecules, rather than what are
effectively cDNA's.


Ewan Birney wrote:

> On Wed, 17 Oct 2001, Heikki Lehvaslaiho wrote:
> > Henry,
> >
> > moltype() is the correct method. It works on EMBL sequences so it should on
> > GenBank, too. I had a look at the code and RNA option was completely
> > ignored.
> > I rewrote the lines doing it and committed them to bioperl-live. I hope you
> > are using CVS and can see the changes immediately.
> >
> > This fix should go into 07 branch, too, but first I'd like to get feedback
> > that the fix really works on larger data sets. I tried it only on t/data
> > examples.
> > Does anyone have a system handy to try this? The potential problem is that
> > it is  DNA/mRNA/... keyword is allowed to be missing completely from the
> > LOCUS line.
> I don't like this. Although genbank says "mRNA" it doesn't *use* RNA
> characters. I'd prefer the mRNA to be somewhere in teh annotation whereas
> moltype means "alphabet".
> It is a "where do you put this information" question. Any other opinions?
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"Speed is subsittute fo accurancy."

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK