[Bioperl-l] How to check mRNA moltype?

[Heikki Lehvaslaiho]

I checked this from Guenter Stoesser, the EMBL Database Coordinator:

There really should be not U residues in entries, ever. The sequence is
always in DNA alphabet. RNA source molecule is indicated by 'RNA' in the ID
line. Thus, moltype() should return 'dna', which it does not at the moment.

Also, the sequence database collaboration has recently stressed that
sequenced_mol qualifier should always be used:

FT   source          1..539
FT                   /db_xref="taxon:3702"
FT                   /sequenced_mol="cDNA to mRNA"
FT                   /organism="Arabidopsis thaliana"

Which means that it is not necessarily used by older entries.

	-Heikki


Heikki Lehvaslaiho wrote:

> EMBL docs state:
> 
> 3.4.1
> Molecule Type: The third item on the line is the type of molecule as stored,
> which  at  present can be either 'DNA', 'RNA' (see the
> comment in Section 2.1 about cDNA) or 'XXX' for unknown molecule type.
> 
>  ... and ...
> 
> 2.1.
> The sequences are presented in the database in a form corresponding to the
> biological state of the information in vivo. Thus, cDNA
> sequences are stored in the database as RNA sequences, even though they
> usually appear in the literature as DNA.
> 
> http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-id+2ke6D1HP2PN+-e+[EMBL:'AB017977']
> --
> 
> Actually, I do not think the above statement holds any more. Check any RNA
> sequence and you will not find U characters.
> 
> I do not have time check it, but I think the feature table source key holds
> the information of the 'topology of molecule sequenced' in all sequence
> databses ( DDBJ/EMBL/GenBank ).
> 
>         -Heikki
> 
> --
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>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________