[EMBOSS] Question regarding Reference Sequence Database

Peter Rice pmr at ebi.ac.uk
Thu Nov 30 14:36:06 UTC 2006

Hi Jean,

> Does any program in EMBOSS package can make use of the Reference Sequence
> Databases? I indexed refseq databases with dbxflat and run showfeat against
> them but receive error about has zero length sequence :

The next release will include refseq as a valid sequence format.

You can usually get away with defining the format as Genbank. If that does not 
work please let me know and I will update the refseq format code.

Aha ... but in this case ...

NG_002612 does have zero length. This appears to be one of those entries (the 
EMBL CON division does much the same) that only refer to sequence data in other 
entries. It ends with the line:

CONTIG      join(complement(AC006998.3:2483..110100))

We can try to process these. The database defintion will need to know where to 
look up "AC006998.3" which is where the sequence data ... and all the missing 
features ... should be.

Can you exclude the CON entries from your indexing? if not, we can try excluding 

Hope that helps,


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