[Bioperl-l] How to check mRNA moltype?

Ewan Birney birney@ebi.ac.uk
Wed, 17 Oct 2001 14:15:54 +0100 (BST)

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?