[Bioperl-l] genbank/embl format ebnf or other formal description

Christopher Bottoms molecules at cpan.org
Tue Sep 11 10:10:22 EDT 2012


Dan,

Why not use BioPerl's Bio::SeqIO, which can parse GenBank files?

--Christopher Bottoms

On Fri, Sep 7, 2012 at 10:43 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> Thanks Chris. That's remarkable, so many words and not an actual formal
> specification. I guess I have some work ahead of me. I found the
> example, but examples rarely contain all edges and corners.
>
> Dan
>
> On Sat, 2012-09-08 at 03:39 +0000, Fields, Christopher J wrote:
>> Re: Genbank, the only know specification I know of is for the feature
>> table portion of the format as you have below.  They do have a
>> (possibly out of date) example file, note it isn't easily found unless
>> you search for it:
>>
>>     http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord
>>
>> EMBL is better in this regard:
>>
>>     http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>>
>> Note that UniProt Knowledgebase also has a user manual outlining the
>> similarities and differences with EMBL:
>>
>>     http://web.expasy.org/docs/userman.html
>>
>> chris
>
>
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