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Guest, Simon | 1 May 2012 05:29
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Re: Circular dependency problems packaging BioPerl as RPM

> -----Original Message-----
> From: Fields, Christopher J [mailto:cjfields <at> illinois.edu]
> Sent: Tuesday, 1 May 2012 1:43 a.m.
> To: Guest, Simon
> Cc: bioperl-l <at> lists.open-bio.org
> Subject: Re: [Bioperl-l] Circular dependency problems packaging BioPerl as
> RPM
> 
> The Bio::Expression dependencies are unusual, I'll have to look through and
> find the modules responsible for pulling these in.  When I last ran these no
> tests failed, so either the dependency is off or no tests have been written for
> the modules in question.
> 
> We can always release a new CPAN BioPerl-Run to deal with it.

Hi Chris,

I ignored the Bio::Expression dependencies and everything eventually built OK, using BioPerl-1.6.901
and  BioPerl-Run-1.006900.

If you release a new BioPerl-Run, I would be interested in packaging it, as I have come this far.

Do you have any ideas about where I could submit the BioPerl and dependency RPMs I built for CentOS 6?  I now
have around 40 RPMs that weren't in CentOS or EPEL, which were all built straight from CPAN using cpanspec. 
I guess others might like to benefit from this (and it would also serve to validate the builds).

My other unknown is what non-Perl dependencies I should add to the BioPerl RPM.  I don't know what to do here. 
The dependencies page on the BioPerl Wiki seems to list only Perl module dependencies.

cheers,
(Continue reading)

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tarakaramji M | 2 May 2012 15:14
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to retrieve Upstream and downstream genes -Reg

Dear all,
I am new to use bioperl modules. Could please guide me retrieving the
upstream and downstream genes of a operon if a set of sequences or
Accession numbers are given.
Thanks in advance

--

-- 
M. Taraka Ramji
Int. PhD
Department of Biological Sciences
Indian Institute of Science Education and Research kolkata
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Carnë Draug | 2 May 2012 16:20
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Re: to retrieve Upstream and downstream genes -Reg

On 2 May 2012 14:14, tarakaramji M <tarakaramji <at> gmail.com> wrote:
> Dear all,
> I am new to use bioperl modules. Could please guide me retrieving the
> upstream and downstream genes of a operon if a set of sequences or
> Accession numbers are given.
> Thanks in advance

Hi Tarak,

Look into the bp_genbank_ref_extractor script (which is already in
bioperl https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl
). You can configure how much downstream and upstream base pairs to
get, just read the documentation.
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Hermann Norpois | 2 May 2012 19:42

get geneID for gene names

Hello,

I wish to get gene IDs for gene names (e.g. bdnf, copg). I thought it was a
good idea to use Bio::DB::EUtilities (see below) and addressed UNISTS as
database because there it was quite easy to find the gene ID. So far I was
unable to retrieve the gene ID from UNISTS. Could anybody give me a hint
how to proceed? The cookbook ... Yes, I was trying.

#!/bin/perl -w

use Bio::DB::EUtilities;

my $name = "Copg";
my $factory = Bio::DB::EUtilities->new(-eutil  => 'efetch',
                                       -db     => 'unists',
                                       -term   => '$name AND mouse [ORGN]',
                                       -email  => 'hnorpois <at> mpipsykl.mpg.de'
                                       )

Thank you
Hermann Norpois
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Fields, Christopher J | 2 May 2012 19:55
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Re: get geneID for gene names

Hermann,

The below works for me (note I'm using esearch, not efetch).  To actually get the records you will use efetch
and the IDs obtained below.

chris

------------------------------
my $name = "Copg";
my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
                                      -db     => 'unists',
                                      -term   => '$name AND mouse [ORGN]',
                                      -email  => '<EMAIL_HERE>',
                                      );

print join(',',$factory->get_ids)."\n";

On May 2, 2012, at 12:42 PM, Hermann Norpois wrote:

> Hello,
> 
> I wish to get gene IDs for gene names (e.g. bdnf, copg). I thought it was a
> good idea to use Bio::DB::EUtilities (see below) and addressed UNISTS as
> database because there it was quite easy to find the gene ID. So far I was
> unable to retrieve the gene ID from UNISTS. Could anybody give me a hint
> how to proceed? The cookbook ... Yes, I was trying.
> 
> #!/bin/perl -w
> 
> use Bio::DB::EUtilities;
(Continue reading)

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Fields, Christopher J | 2 May 2012 20:03
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Re: get geneID for gene names

Also, a small but very significant bug is in the below.  Can you spot it?

The '-term' value is in single quotes, these need to be double-quotes to interpolate $name.  Otherwise, it
is literally looking for '$name'.

chris

On May 2, 2012, at 12:55 PM, Christopher Fields wrote:

> Hermann,
> 
> The below works for me (note I'm using esearch, not efetch).  To actually get the records you will use efetch
and the IDs obtained below.
> 
> chris
> 
> ------------------------------
> my $name = "Copg";
> my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
>                                      -db     => 'unists',
>                                      -term   => '$name AND mouse [ORGN]',
>                                      -email  => '<EMAIL_HERE>',
>                                      );
> 
> print join(',',$factory->get_ids)."\n";
> 
> 
> On May 2, 2012, at 12:42 PM, Hermann Norpois wrote:
> 
>> Hello,
(Continue reading)

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Hermann Norpois | 2 May 2012 23:00

Re: get geneID for gene names

Thank you very much. But there still is a problem.

This is my output:
525211,210532,167498,142652

I get some ids (the first one is the UniSTS ID, the following ... I do not
know) but there is no gene ID. If you compare to the following link:
http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=525211 The gene ID
should be 54161<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=54161>
.

This is my (your) script:

#!/bin/perl -w

use Bio::DB::EUtilities;

my $name = "Copg";
my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
                                     -db     => 'unists',
                                     -term   => "$name AND Mus musculus
[ORGN]",
                                     -email  => 'hnorpois <at> mpipsykl.mpg.de',
                                     );

print join(',',$factory->get_ids)."\n";

2012/5/2 Fields, Christopher J <cjfields <at> illinois.edu>

> Also, a small but very significant bug is in the below.  Can you spot it?
(Continue reading)

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Smithies, Russell | 3 May 2012 01:12
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Re: get geneID for gene names

If you're looking for gene information, why are you searching UniSTS?
Unless I've overlooked something, wouldn't it be more useful to search the "gene" database and tighten up
your query a bit?

#!/bin/perl 
use strict;
use warnings;

use Bio::DB::EUtilities;

my $factory = Bio::DB::EUtilities->new(
    -eutil      => 'esearch',
    -db         => 'gene',
    -term       => '(copg[Gene Name]) AND mouse[Organism]',
    -email      => 'hnorpois <at> mpipsykl.mpg.de',
    -usehistory => 'y'
);

my $hist = $factory->next_History || die "No history data returned";

$factory->set_parameters(
    -eutil   => 'efetch',
    -history => $hist
);

print $factory->get_Response->content;

--Russell

-----Original Message-----
(Continue reading)

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Prasad ms | 4 May 2012 07:13
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About bioperl global alignment

Hello sir,
I am Prasad, student of MS in bioinformatics. I am doing my final year
project, and sequence alignment is the part of my project. I am having
nearly 50k sequences and i want to do a pairwise global alignment (NW
alignment). I read the bioperl tutorial. But in that there is no mention
about this. Could you please guide how can i do this type of alignment
using bioperl.
I assure that all the usage is purely for academic.

Looking forward  to hear from you.

Thank you,

Regards,
Prasad MS
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Frank Schwach | 4 May 2012 08:31
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Re: About bioperl global alignment

Hi Prasad,

have a look at this:
http://www.bioperl.org/wiki/HOWTO:AlignIO_and_SimpleAlign#Aligning_multiple_sequences_with_Clustalw.pm_and_TCoffee.pm

The HOWTO pages are a brilliant source of information and starting 
points for your own scripts.
The main point here is: Bioperl doesn't do any alignment. It provides 
the tools to automate making alignments (or other things) with 
third-party software such as ClustalW or TCoffee as described in the 
text. You need to install those programs locally and then use Bioperl to 
go fetch sequences form your FASTA (or whatever format) sequence files 
and run them through the aligner, then use more Bioperl methods to 
extract data from the alignments and generate your final results. That 
makes it possible, for example, to write a script that extracts every 
possible pair of sequences from a FASTA file and run them through 
ClustalW, then analyse the results and record the percent identity or 
whatever you are interested in and generate a spreadsheet with your 
final results, ready to be sent to Nature :-) !!!! Feel free to ask if 
you need more help.

Good luck!

Frank

On 04/05/12 06:13, Prasad ms wrote:
> Hello sir,
> I am Prasad, student of MS in bioinformatics. I am doing my final year
> project, and sequence alignment is the part of my project. I am having
> nearly 50k sequences and i want to do a pairwise global alignment (NW
(Continue reading)

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