bill | 1 Jun 06:28 2008

Re: How to extract list of SNPs for a given gene?

Hi, Abhijit,

Gene2Snp, a standalone application which find SNPs for given Entrez Genes,
can be freely downloaded from
http://www.genenformics.com/download.html

A sample output is available at
http://www.genenformics.com/Gene2Snp_example_result.txt

This application may consume lots of CPU/memory due to complexity of locus
region.

Bill <at> genenformics.com

> From: artendulkar <at> gmail.com [mailto:artendulkar <at> gmail.com]
> Sent: Tuesday, May 20, 2008 4:21 PM
> To: bioperl-l <at> lists.open-bio.org
> Subject: [Bioperl-l] How to extract list of SNPs for a given gene?
>
> Hi,
> Can anyone please tell me how to get list of SNPs in any particular gene
> using BioPerl, given NCBI Gene ID?
> Is there any method, which takes NCBI gene ID as argument and returns
> list
> of SNPs by connecting to dbSNP?
> Thank you.
> Abhijit
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
(Continue reading)

Chris Fields | 1 Jun 18:51 2008
Picon

Re: Fwd: BPlite

The problem is BPLite has been officially deprecated in favor of  
Bio::SearchIO BLAST parsing (including Sendu's BLAST-based pull  
parser).  If there is interest in resurrecting BPLite we would need  
someone to actively maintain it.

chris

On May 31, 2008, at 4:53 PM, Jason Stajich wrote:

>
>
> Begin forwarded message:
>
>> From: Anatoly Urisman <urisman <at> gmail.com>
>> Date: May 31, 2008 5:08:03 AM CDT
>> To: jason...
>> Subject: BPlite
>>
>> Hi Jason,
>> I was wondering if you are aware of a fix to the BPlite.pm module  
>> that supports the new NCBI blastall output (i.e. reports are not  
>> delimited by something like BLASTN 2.2.8 [Jan-05-2004]).
>> Thanks.
>> Anatoly Urisman, MD-PhD
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

(Continue reading)

Chris Fields | 3 Jun 17:25 2008
Picon

[ANNOUNCEMENT] BioPerl and the Google Summer of Code

On behalf of the BioPerl core developers, Google, and the National  
Evolutionary Synthesis Center (NESCent), I would like to congratulate  
Mira Han on being accepted as a student for the Google Summer of Code  
(GSoC) and welcome her to the BioPerl community.  Mira's accepted  
project proposal involves developing phyloXML support for BioPerl.   
Following is the proposal abstract:

"PhyloXML is an XML document model for phylogenetic data that  
incorporates various annotation types, including user customized data.  
The format is currently not supported by BioPerl. I propose a SAX  
based data structure and interface for PhyloXML support in BioPerl. I  
will use most of the existing IO structures such as TreeIO and  
TreeEventBuilder and subclass them to extend the functions specific to  
PhyloXML. The objects will be connected to various existing BioPerl  
modules, such as SeqI, TaxonI, AnnotationI by reference in order to  
accommodate different phyloXML elements."

NESCent, under the Phyloinformatics Summer of Code, is participating  
as a mentoring organization in the GSoC for the second year.  This  
year, five projects (including Mira's) are being funded by Google,  
with a sixth project being funded by external sources.  Mira's co- 
mentors for this project are myself, Jason Stajich, Rutger Vos, and  
Christian Zmasek (the primary developer of phyloXML).  However, I  
encourage Mira to ask questions on the BioPerl mail list for feedback  
from the greater BioPerl community.

Further information on phyloXML:

http://www.phyloxml.org/

(Continue reading)

miraceti | 3 Jun 17:58 2008
Picon

Re: [ANNOUNCEMENT] BioPerl and the Google Summer of Code

Thanks for the welcome,
I'm very excited to be part of the great community,
Here is the wiki page for the project,
*http://www.bioperl.org/wiki/PhyloXML_support_in_BioPerl
*I'll look forward to interacting with you and getting lots of help!

Mira Han

On Tue, Jun 3, 2008 at 11:25 AM, Chris Fields <cjfields <at> uiuc.edu> wrote:

> On behalf of the BioPerl core developers, Google, and the National
> Evolutionary Synthesis Center (NESCent), I would like to congratulate Mira
> Han on being accepted as a student for the Google Summer of Code (GSoC) and
> welcome her to the BioPerl community.  Mira's accepted project proposal
> involves developing phyloXML support for BioPerl.  Following is the proposal
> abstract:
>
> "PhyloXML is an XML document model for phylogenetic data that incorporates
> various annotation types, including user customized data. The format is
> currently not supported by BioPerl. I propose a SAX based data structure and
> interface for PhyloXML support in BioPerl. I will use most of the existing
> IO structures such as TreeIO and TreeEventBuilder and subclass them to
> extend the functions specific to PhyloXML. The objects will be connected to
> various existing BioPerl modules, such as SeqI, TaxonI, AnnotationI by
> reference in order to accommodate different phyloXML elements."
>
> NESCent, under the Phyloinformatics Summer of Code, is participating as a
> mentoring organization in the GSoC for the second year.  This year, five
> projects (including Mira's) are being funded by Google, with a sixth project
> being funded by external sources.  Mira's co-mentors for this project are
(Continue reading)

Arkady | 3 Jun 22:50 2008
Picon

liftOver API

Hi folks,

I've seen references occasionally to ensembl API or a BioPerl module
for converting between (human) genome assemblies (e.g. hg17 to hg18).
I'm also, of course, aware of liftOver, and of the chain file format.
But I'm more interested in the API. Does this still exist? Where can I
find it?

If not, does anyone have something that does this?

Cheers,
John Woods
Ousmane Diallo | 3 Jun 23:21 2008
Picon

How to get protein ID and get protein accession from GI

hello,
Could somebody help me on how to get the protein ID and ACCESSION using the mRNA gi or accession.

my $db_obj = Bio::DB::GenBank->new();    
my $seq_obj = $db_obj->get_Seq_by_acc('123456') ;   # I pass here the mrna acc to get the seq_obj
my $gi = $seq_obj->primary_id ;                     # I get here the gi

I need to get the protein ID and protein ACCESSION"

THANKS!!
Pallavi Sarmah | 4 Jun 14:33 2008
Picon

Bioperl-ext installation error


Hi,
I am trying to install Bioperl-ext and when rum the Makefile.PL it gives me the following error. 

ERROR from evaluation of
/home/pallavi/Pallavi/downloads/bioperl-ext-1.5.1/Bio/SeqIO/staden/Makefile.PL: Invalid
version '' for Bio::SeqIO::staden::read.

Can anyone let me know the remedy for this. I stuck with this for last 2-3 days.

Pallavi
Siddhartha Basu | 4 Jun 16:54 2008
Picon

Re: How to get protein ID and get protein accession from GI

Hi,
You have to get the 'Feature' object for that.

On Tue, 03 Jun 2008, Ousmane Diallo wrote:

> hello,
> Could somebody help me on how to get the protein ID and ACCESSION using the mRNA gi or accession.
>
>
> my $db_obj = Bio::DB::GenBank->new();    my $seq_obj = 
> $db_obj->get_Seq_by_acc('123456') ;   # I pass here the mrna acc to get the 
> seq_obj
> my $gi = $seq_obj->primary_id ;                     # I get here the gi

my ($feat) = grep { $_->primary_tag() eq 'Protein' } $seq_obj->get_SeqFeatures();
print $feat->seq_id(),"\n";

For details and explanations read the Howto here .....

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

-siddhartha

>
>
> I need to get the protein ID and protein ACCESSION"
>
> THANKS!!
>
> _______________________________________________
(Continue reading)

Jay Hannah | 4 Jun 16:19 2008
Picon

Re: How to get protein ID and get protein accession from GI

On Jun 3, 2008, at 4:21 PM, Ousmane Diallo wrote:
> Could somebody help me on how to get the protein ID and ACCESSION  
> using the mRNA gi or accession.
>
> my $db_obj = Bio::DB::GenBank->new();
> my $seq_obj = $db_obj->get_Seq_by_acc('123456') ;   # I pass here  
> the mrna acc to get the seq_obj
> my $gi = $seq_obj->primary_id ;                     # I get here  
> the gi
>
> I need to get the protein ID and protein ACCESSION"

Please provide a real MRNA accession # you're interested in. I prefer  
sending example code that I know actually works on your data of  
interest.  :)

Thanks,

j
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah
bill | 5 Jun 07:16 2008

Re: How to get protein ID and get protein accession from GI

Hi, Ousmane,

IdConvert, a standalone application which convert protein/nucleotide
gi/acc, can be freely downloaded from
http://www.genenformics.com/download.html

A sample output is available at
http://www.genenformics.com/IdConvert_example_result.txt

The following is a test run:
>IdConvert.exe 300,NM_005252,399,NP_001225
#Input	Nuc_GI	Nuc_Acc	Pro_GI	Pro_Acc	Desc
300	299	X59693.1	300	CAA42214.1	ubiquinol--cytochrome c reductase [Bos
taurus]
NM_005252	6552332	NM_005252.2	4885241	NP_005243.1	v-fos FBJ murine
osteosarcoma viral oncogene homolog [Homo sapiens]
399	399	V00111.1	400	CAA23445.1	unnamed protein product [Bos taurus]
NP_001225	15451858	NM_001234.3	4502589	NP_001225.1	caveolin 3 [Homo sapiens]

Bill <at> genenformics.com

> hello,
> Could somebody help me on how to get the protein ID and ACCESSION using
> the mRNA gi or accession.
>
>
> my $db_obj = Bio::DB::GenBank->new();
> my $seq_obj = $db_obj->get_Seq_by_acc('123456') ;   # I pass here the mrna
> acc to get the seq_obj
> my $gi = $seq_obj->primary_id ;                     # I get here the gi
(Continue reading)


Gmane