[EMBOSS] seqret

[Stefanie De Bodt]

Peter Rice wrote:

> Stefanie De Bodt wrote:
>
>> seqret -feature -sequence DBname:AC -outseq embl:AC.embl
>>
>> I get several warnings and I can´t figure out what the reason for 
>> these warnings is.
>>
>> Warning: bad /cons_splice value '(5'site:YES,'
>> Warning: PVU13023: Bad value '(5'site:YES,' for tag '/cons_splice'
>>
>> Could you help me with this problem, is there a mistake in the 
>> command line or is it due to something else?
>
>
> EMBOSS validates the EMBL feature table syntax, using a reasonably 
> up-to-date version of the EMBL feature table document (I do have some 
> minor updates to add for the latest version).
>
> Is this your own database, or is this an EMBL entry?

I downloaded the database just recently from the NCBI FTP site. It is 
the database that contains all plant nucleotide sequences.

>
> These are only warnings ... but I would be interested to see the 
> output of entret (the complete text of the entry as read by EMBOSS) to 
> check the feature validation is correct.

Indeed, only warnings.The output file seems OK. I have attached it.

thanks,

Stefanie De Bodt

>
> regards,
>
> Peter Rice
>
>

-- 
Stefanie De Bodt
Research Group of Bioinformatics and Evolutionary Genomics
Department of Plant Systems Biology
Ghent University - Flemish Institute for Biotechnology (VIB)
Technologiepark 927, B-9052 Ghent, BELGIUM

Tel: +32 (0)9 3313692
Fax: +32 (0)9 3313809

stefanie.debodt at psb.ugent.be
http://www.psb.ugent.be/bioinformatics

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