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
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Try the new software tools for yourself. Speed compiling, find bugs
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