[BiO BB] RefSeq mRNA sequences of barley

Mike Marchywka marchywka at hotmail.com
Tue Jul 24 14:19:06 EDT 2007

What have you got against downloading the whole genome? I didn't see
it at ensembl but, as you probably know, ag plant genomics is
a big deal economically. The USDA and ARS probably have more stuff like
this ( first thing I found on google).


Offhand, it looks like you have mutually exclusive [prop] criteria as prop 
and properties
are synonyms ( but usually the query dump tells you howmany hits on each 
term ):

Usually eutils provides parse info that you can sort out when query results 
make sense but I've only used this from pubmed and the response from
nucleotide was unhelpful- you can probably get a dump from the web page
but I've never used it.

$ eutilsnew -v  -out asdf -dump "barley AND smith[AU] "
<?xml version="1.0"?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" 
<WebEnv>09zlDsvf9Apq_WlB1MrLvNbMDVmdMFyE-0fh8eDgZhtQlZKxV5kTGmzUJpJ at 1FBF
                        <To>(("hordeum"[TIAB] NOT Medline[SB]) OR 
t;hordeum"[MeSH Terms] OR barley[Text Word])</To>

The NCBI web interface is usually quite good but I ran into a similar 
with blast databases. I finally found their list for blasting,


and added to my script,

$ blastnew -help db | grep -i barley
   genomes  barley          barley

Before I found this, I complained that their example db names weren't right
and I even had to reverse engineer a piece of their html. Try googling 
to their site, site:nih.gov

Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
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marchywka at hotmail.com

>From: "George Tzanis" <gtzanis at csd.auth.gr>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "'General Forum at Bioinformatics.Org'" 
><bio_bulletin_board at bioinformatics.org>
>Subject: [BiO BB] RefSeq mRNA sequences of barley
>Date: Sat, 21 Jul 2007 23:38:42 +0300
>Dear All,
>I would like to get all the non-redundant cDNA sequences of barley.
>For this reason I'm thinking about retrieving all RefSeq mRNAs of
>barley. I have made a search to the Core Nucleotide database
>(http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore) using the
>following query:
>"barley[organism] AND biomol_mRNA[properties] AND srcdb_refseq[PROP]"
>However, not any sequences were returned. I have also used the Entrez
>Limits settings, but the result was the same.
>Is there something wrong in my search?
>Are there any RefSeq mRNAs for barley?
>Is there another way to get a non-redundant set of cDNA (or mRNA)
>sequences of barley? I will appreciate any idea.
>Thank you in advance,
>George Tzanis
>Department of Informatics
>Aristotle University of Thessaloniki
>54124 Thessaloniki
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org


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