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From: Jason Stajich <jason.stajich <at> gmail.com>
Subject: Re: get CDS start site for entry in NCBI
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Friday 19th April 2013 19:32:32 UTC (over 5 years ago)
you want to loop through all the features and get the ones which are cds
and then in this case get the start of the feature. The code for that is:

for my $feat ( $seq->get_SeqFeatures() ) {
 If( $feat->primary_tag eq 'CDS' ) {
   print $feat->start, "\n";
On Apr 17, 2013, at 7:08 PM, Matthew McCormack

> I am not much of a Perl coder and I have a few questions.
>     First, I would like to write a script that will go to NCBI genebank
and get the base number for the start of the CDS region, e.g. 235 (given a
particular accession number). I have looked at HOWTO's and documentation
for Bio::SeqIO and Bio::DB::GenBank and I can cut and paste the examples
and they work, but I can not figure out how to get what I want; the CDS
start site. I have difficulty knowing what all the methods and their
options are for the seqio object and seq_object. Most of the examples seem
to be using a file to get information and not a website.
>   Actually, what I have to start with is a TAIR locus number such as
AT4g08500, but I can not search on this at NCBI and come up with a unique
entry. I may have to have a table of conversions from TAIR locus number to
accession numbers.
>  Also, I was looking for a bit of advice. What I am doing is getting data
off another web site. I have a script using the WWW::Mechanize module in
which I can input a link and go to that webpage, and then go down a line of
links (over 100) getting information from each link. As part of that
information that I am getting is the number base of a binding site, but I
want to know if that binding site is in the CDS. The start number is the
start of the gene, so say if the binding site is 235, then I want to know
if this is in the CDS. This data is not provided by the website, that is
why I want to go to NCBI and get the start of the CDS. The data at NCBI for
'gene' has the same length as the first webpage, but also contains the
beginning of the CDS, say 299, so with this information I can tel
 l if the binding site is in the CDS. Do you think the best way to do this
is extract the info from the link on the first web page, then go to NCBI
and extract the CDS, then back to the orig!
 inal web page and the next link, and so on, for a couple of hundred links
? Or is there a better way ? I am concerned about a script that will keep
going back to NCBI.
> Matthew
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Jason Stajich
[email protected]
[email protected]
CD: 4ms