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Hi Pengfei,<br>
<br>
Depending on the species and data, it is not always possible to have
an official gene name and/or description.<br>
<br>
As more proteins and cDNAs are submitted to public databases, we
will be able to use these to name the gene models.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 11/02/2014 01:25, ÁõÅô·É wrote:<br>
</div>
<blockquote
cite="mid:CAH_jMvsG-CpT4HNYFASxXX6kYuyET8JZmVcPfo181XcjuyrC2w@mail.gmail.com"
type="cite">
<div dir="ltr">Thanks, now I am analyzing RNAseq data and want to
download the gene information of the species, so briefly now I
need the gene name, production function or description, stable
id and gene length data.</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2014-02-10 17:10 GMT+08:00 mag <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi Pengfei,<br>
<br>
I am not entirely sure which data you are looking at, but
depending on the databases, not all genes will have a
description or an external_name.<br>
<br>
For a given gene, we assign a display xref if we find an
external reference from a trusted source matching the
ensembl gene.<br>
That xref (external reference) is then used to assign a
display name to the gene.<br>
If there is no such external reference, the gene will have
no display name and we will use the ensembl stable id
instead.<br>
<br>
A similar rule applies to assigning descriptions.<br>
<br>
<br>
Hope that helps,<br>
Magali
<div>
<div class="h5"><br>
<br>
<div>On 10/02/2014 05:22, ÁõÅô·É wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Magali and <br>
</div>
<div>Hi all,<br>
<br>
</div>
<div>I use following code to fetch all information
of genes for a bacteria, but get some errors
(althouth I could get all data I wanted), but I
could not figure out where goes wrong, thanks:<br>
</div>
<div>errors:<br>
Use of uninitialized value in print at
HZ254_genedata.pl line 20.<br>
<br>
scripts:<br>
# methanocella_conradii_hz254 <br>
#HZ254_genedata.pl<br>
#!/usr/bin/perl<br>
use strict;<br>
use warnings;<br>
use Bio::EnsEMBL::LookUp;<br>
# load the lookup from the main Ensembl Bacteria
public server<br>
my $lookup = Bio::EnsEMBL::LookUp->new(<br>
-URL => "<a moz-do-not-send="true"
href="http://bacteria.ensembl.org/registry.json"
target="_blank">http://bacteria.ensembl.org/registry.json</a>",<br>
-NO_CACHE => 1<br>
);<br>
# find the correct database adaptor using a
unique name<br>
my ($dba) = @{$lookup->get_by_name_exact(<br>
'methanocella_conradii_hz254'<br>
)};<br>
my $genes =
$dba->get_GeneAdaptor()->fetch_all(); <br>
# get all gene infomation<br>
open (MYFILE, '>>HZ254gene_data.txt');<br>
foreach my $gene (@$genes){<br>
print $gene->stable_id,"\t", <br>
$gene->display_id,"\t",<br>
$gene->description,"\t", <br>
$gene->start, " - ", <br>
$gene->end, "\t", <br>
$gene->external_name, "\t",<br>
$gene->length,"\n";<br>
};<br>
close (MYFILE);<br>
</div>
<div>##API version 74<br>
<br>
</div>
<div>
<div>
<div><br>
-- <br>
<div>Pengfei Liu, PhD Candidate<br>
<br>
Lab of Microbial Ecology<br>
College of Resources and Environmental
Sciences<br>
China Agricultural University<br>
No.2 Yuanmingyuanxilu, Beijing, 100193<br>
P.R. China<br>
<br>
Tel: +86-10-62731358<br>
Fax: +86-10-62731016<br>
<br>
E-mail: <a moz-do-not-send="true"
href="mailto:liupfskygre@gmail.com"
target="_blank">liupfskygre@gmail.com</a></div>
<div> </div>
<div>If you are afraid of tomorrow, how can
you enjoy today! </div>
<div>Keep hungry, Keep foolish! </div>
<div>Moving forward!</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>Pengfei Liu, PhD Candidate<br>
<br>
Lab of Microbial Ecology<br>
College of Resources and Environmental Sciences<br>
China Agricultural University<br>
No.2 Yuanmingyuanxilu, Beijing, 100193<br>
P.R. China<br>
<br>
Tel: +86-10-62731358<br>
Fax: +86-10-62731016<br>
<br>
E-mail: <a moz-do-not-send="true"
href="mailto:liupfskygre@gmail.com" target="_blank">liupfskygre@gmail.com</a></div>
<div> </div>
<div>If you are afraid of tomorrow, how can you enjoy today! </div>
<div>Keep hungry, Keep foolish! </div>
<div>Moving forward!</div>
</div>
</blockquote>
<br>
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