The link to find more info about eSearch can be found here instead:
http://www.ncbi.nlm.nih.gov/corehtml/query/static/esearch_help.html
Franck
On 26 February 2010 10:17, Franck Tanoh <[email protected]> wrote:
> Hi,
>
> >Is there another database that I should be querying if I want to find a
> >list homologous genes for a list of species?
> Try the homologene database from the NCBI:
> http://www.ncbi.nlm.nih.gov/homologene .
> It's one the database compatible with eSearch. A complete list of all the
> database you can use with eSearch is here:
> http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?
> Another useful link to find more information about eSearch:
> http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?
>
> >Or, is there some way to match these up to find out which are homologous?
> For this option, you may need to write some beanshell script:
> http://www.mygrid.org.uk/usermanual1.7/beanshell_processor.html
>
> Hope that helps
>
> Franck
>
>
>
>
>> ---------- Forwarded message ----------
>> From: <[email protected]>
>> Date: Wed, Feb 24, 2010 at 06:57
>> Subject: [Taverna-users] Sorting an esearch query into homologous genes.
>> To: [email protected]
>>
>>
>> Hi,
>> I am working on creating a workflow that gets all of the nucleotide
>> fasta sequences for species of mayflies and conducts alignment and
>> phylogenetic analyses on them.
>> In my local database I entered all of the species that I want to
>> analyze and I do an esearch query for each one: Ephemera
>> strigata"[Organism]
>> I am using this webservice:
>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl
>> run_eSearch
>>
>> This gives me back several lists with genes for each species. The
>> problem is that the result does not show me the name of the gene in
>> any standardized way. I may see 18s ribosomal mentioned in the
>> description but I don't see a standardized way of knowing which of
>> these genes are homologous across species.
>> My goal is to find all of the genes that appear in say 3 or more of
>> the species I am analyzing and construct a dataset with those. Is
>> there another database that I should be querying if I want to find a
>> list homologous genes for a list of species? Or, is there some way to
>> match these up to find out which are homologous?
>>
>>
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>>
>>
>>
>> --
>> Stian Soiland-Reyes, myGrid team
>> School of Computer Science
>> The University of Manchester
>>
>
>
>
> --
> "Science knows no country, because knowledge belongs to humanity, and is
> the torch which illuminates the world." - Louis Pasteur
>
--
"Science knows no country, because knowledge belongs to humanity, and is the
torch which illuminates the world." - Louis Pasteur
------------------------------------------------------------------------------
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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