[Biojava-l] Genebank Webservices ?

Richard Holland holland at eaglegenomics.com
Thu Jan 8 11:07:43 UTC 2009

There is no generic interface to NCBI eUtils in BioJava, but one is planned.

In the meantime take a look at this existing BioJava 1.6 package, which
will query Genbank for a sequence and return a BioJava RichSequence
object containing the result. You can then search through the
annotations and features of the sequence to find the result you need.

This is for Gene records:


Or the equivalent for Peptide records:



Ashika Umanga Umagiliya wrote:
> Greetings all,
> I come from a computer science background and only have little knowledge
> in bioinformatics.
> In the application I develop,I want to search for an genebank id (like
> 4558277) from ncbi and want to retrieve the relavent PDB_ID.
> For example :
> Say for id '4558277', i get the result
> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=4558277
> I can see the value '1F58_L' which is only significant to me.
> I want to know where there is any webservice to do retrive this
> information.
> That means, I send '4558277'  in SOAP input parameters and in the result
> I should get the value '1F58_L' .
> I found following webservices and want to know whether I can use the one
> for 'Gene' :
> http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html
> thanks in advance,
> umanga
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Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com

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