[Bioperl-l] Question about embl format

[Ewan Birney]

On Thu, 17 Apr 2003, Lincoln Stein wrote:

> Hello,
> 
> The "sequence dumper" plugin for the Generic Genome Browser has been crashing 
> when making an EMBL dump of a particular region of the worm genome.  The 
> issue is a "Transposon_insertion" feature, which exceeds the 15 character 
> limit for EMBL feature tags.  If I remove the Bio::SeqIO::embl check for this 
> limit, I get an output that looks like this:
> 
> ...
> FT   Transposon_insertion complement(13204595..13204596)
> FT                   /score=""
> FT                   /group="cxP4108"
> FT                   /id=7726466
> FT                   /method="Transposon_insertion"
> FT                   /source="Allele"
> FT                   /phase=""
> FT   repeat          13204572..13204602
> FT                   /score=80
> FT                   /group=""
> FT                   /notes="loop 283"
> FT                   /id=7775180
> FT                   /method="repeat"
> FT                   /source="inverted"
> FT                   /phase=""
> FT                   /note="score=80"
> ...
> 
> My question is whether this is acceptable embl format?  If not, I will have to 
> truncate feature type names at 15 characters, but this is going to lose 
> information.


Looks like the defn says <15 letters

Feature table components, including feature keys, qualifiers, accession 
numbers, database name abbreviations, feature labels, and location 
operators, are all named following the same conventions. Component names 
may be no more than 20 characters long  (Feature keys 15, Feature 
qualifiers 20)  and must contain at least one letter. While case should 
not be regarded as significant in comparing feature labels ('Prot1' and 
'pROT1' are the same), the databanks will preserve the case of labels as 
originally annotated. The following characters are permitted to occur in 
feature table component names: 



From:


http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html



> 
> Lincoln
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
> 
> 
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