[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).

http://harvest.ucr.edu/

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 ):
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpentrez.table.EntrezHelp.T7



Usually eutils provides parse info that you can sort out when query results 
don't
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" 
"htt
p://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">
<eSearchResult>
        <Count>98</Count>
        <RetMax>1</RetMax>
        <RetStart>0</RetStart>
        <QueryKey>1</QueryKey>
        
<WebEnv>09zlDsvf9Apq_WlB1MrLvNbMDVmdMFyE-0fh8eDgZhtQlZKxV5kTGmzUJpJ at 1FBF
437C6A641A70_0045SID</WebEnv>
        <IdList>
                <Id>17609926</Id>
        </IdList>
        <TranslationSet>
                <Translation>
                        <From>barley</From>
                        <To>((&quot;hordeum&quot;[TIAB] NOT Medline[SB]) OR 
&quo
t;hordeum&quot;[MeSH Terms] OR barley[Text Word])</To>
                </Translation>
        </TranslationSet>
        <TranslationStack>
                <TermSet>
                        <Term>&quot;hordeum&quot;[TIAB]</Term>
                        <Field>TIAB</Field>
                        <Count>2045</Count>
                        <Explode>Y</Explode>
                </TermSet>
                <TermSet>



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

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_accessible_blastdblist.html

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 
confined
to their site, site:nih.gov





Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
404-788-1216 (C)<- leave message
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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
>Greece
>_______________________________________________
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

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