[Bioperl-l] split location problems

Nadeem Faruque faruque at ebi.ac.uk
Tue Oct 17 04:19:44 EDT 2006


EMBL' currently outputs join-complements in the format
join(complement(30..40),complement(10..20))
instead of the Genbank preferred
complement(join(10..20,30..40))

EMBL's may reflect what happens in the cell a little more than  
Genbank's, but it is less readable and less concise.
NB I've also seen a couple of people construct these incorrectly
eg join(complement(10..20),complement(30..40))

I believe we are moving to the complement-join format but I can't  
give a date for the transition.

Having said that, trans-splicing will still give us the joys of  
complex locations,
eg
join(1..5,complement(join(10..20,30..40)))
complement(join(30..40,10..20)) <- looks wrong (unless it is a very  
small circle) but mis-ordered exons are resolved by the trans- 
splicing machinery.

Nadeem


--
S.M. Nadeem N. Faruque
EMBL Nucleotide Database Curation Team
EMBL Outstation
Tel: +44 1223 494611                     Fax: +44 1223 494472
The European Bioinformatics Institute    URL: http://www.ebi.ac.uk/
Email for data submissions: datasubs at ebi.ac.uk
Email for updates: update at ebi.ac.uk
========================================================



More information about the Bioperl-l mailing list