[EMBOSS] A question about CON entries

Peter Rice pmr at ebi.ac.uk
Fri Feb 1 16:55:37 UTC 2008

Guy Bottu wrote:
>     Dear friends,
> As you know, the databanks EMBL, GenBank and RefSeq contain entries that 
> do not contain the sequence itself, but instead "join" information about 
> how to compose the sequence using ranges from other sequences. When the 
> databank has been installed under EMBOSS the sequence is not available, 
> since EMBOSS wil give a "Warning: Sequence has zero length". Do you 
> think that EMBOSS should be able to handle such cases ? And in the 
> meantime, do you know about tools that can, given as input the "CON" 
> sequence and a databank with sequences, assemble on-the-fly the sequence ?

Yes we need to handle those entries. If you want to request this 
feature, please tell us. More requests means higher priority :-)

When reading a CON entry we need a database to use to read the true 
sequence and features.

If we are reading from a database we can add the information in the 
database definition.

How do we define a default to resolve EMBL CON entries?

Can we handle EMBL release and EMBL updates?



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