[Bioperl-l] Accession Nuber to Genbank Record (Isolation Source)

shalabh sharma shalabh.sharma7 at gmail.com
Fri Mar 5 17:57:00 EST 2010


Thanks everyone, i got it what i was looking for.
EUtlities helped me a lot.

Thanks
Shalabh


On Fri, Mar 5, 2010 at 5:06 PM, shalabh sharma <shalabh.sharma7 at gmail.com>wrote:

> Thanks Bran and Chris,
>            I followed the example given here :
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
> to retrieve raw data records from genbank.
> For example i used the id : 157091572 to  get the genbank record, but the
> downloaded file does not contain "isolation_source" which is there when you
> look for the record online:
>
> http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=T2S9N0PJ01N&log%24=nuclalign&blast_rank=1&list_uids=157091572
>
> Thanks
> Shalabh
>
>
> On Fri, Mar 5, 2010 at 4:22 PM, Chris Fields <cjfields at illinois.edu>wrote:
>
>> Regardless on what you try, it will only limit records returned (e.g.
>> you will still get full records, unless you take steps to limit those
>> somehow, by adding sequence start/stop, etc).
>>
>> Anyway, this worked to retrieve those with that tag:
>> "src isolation source"[Properties]
>>
>> That get a lot of hits.
>>
>> If you are only interested in that one line you could just parse it out
>> w/o resorting to bioperl (beleiev it or not, it's not always the best
>> answer).
>>
>> chris
>>
>> On Fri, 2010-03-05 at 15:43 -0500, Brian Osborne wrote:
>> > Shalabh,
>> >
>> > I see. I think you could use EUtils then. Take a look at these:
>> >
>> > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
>> >
>> > http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service
>> >
>> > I'm not an expert on these, and I do not know if one can ask for just a
>> tag value ("isolation_source"). Getting a tag value from the downloaded
>> Genbank entry is not difficult though, that Feature-Annotation HOWTO shows
>> you how.
>> >
>> > Brian O.
>> >
>> >
>>
>> > On Mar 5, 2010, at 3:29 PM, shalabh sharma wrote:
>> >
>> > > HI Brian,
>> > >           Thanks for your quick reply.
>> > > I was reading the document and it think it talks about parsing a
>> GenBank
>> > > record. What i exactly want is to submit a batch of accession numbers
>> and
>> > > get "isolation_source" directly without downloading all the Genbank
>> files.
>> > > I am still reading the document may be i missed something.
>> > >
>> > > Thanks a lot
>> > > shalabh
>> > >
>> > >
>> > > On Fri, Mar 5, 2010 at 3:13 PM, Brian Osborne <bosborne11 at verizon.net
>> >wrote:
>> > >
>> > >> Shalabh,
>> > >>
>> > >> You can start by reading about how Bioperl processes Genbank files
>> and
>> > >> their annotations:
>> > >>
>> > >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>> > >>
>> > >>
>> > >>
>> > >> Brian O.
>> > >>
>> > >> On Mar 5, 2010, at 3:06 PM, shalabh sharma wrote:
>> > >>
>> > >>> Hi All,
>> > >>>       I have a set of accession numbers. Is it possible to get
>> > >>> "isolation_source" from the GenBank records for all the Accession
>> > >> numbers.
>> > >>>
>> > >>> I would really appreciate if anyone can help me out.
>> > >>>
>> > >>> Thanks
>> > >>> Shalabh
>> > >>> _______________________________________________
>> > >>> Bioperl-l mailing list
>> > >>> Bioperl-l at lists.open-bio.org
>> > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> > >>
>> > >>
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>> >
>> >
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>>
>>
>>
>


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