[BiO BB] How to get the gene sequence efficiently

[Ryan Brinkman]

This is something that Ensembl is quite good at, and they have already written the scripts (well the Perl API) for you.  
www.ensembl.org 

Have a browse through their tutorial, which I believe shows examples of what you need.
http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/CodeTutorial.html


Message: 1
Date: Mon, 15 Jul 2002 13:49:22 -0500
From: Chunlei Wu <newgene at bigfoot.com>
To: bio_bulletin_board at bioinformatics.org 
Subject: [BiO BB] How to get the gene sequence efficiently
Reply-To: bio_bulletin_board at bioinformatics.org 

Hi, group,
             I have a problem need the help from the group; it may be 
easy for the experienced experts here.
             I want to get the gene sequences for a list of genes (with 
gene symbol, refseq accession number, etc). I know how to get the gene 
sequence one-by-one from NCBI's genome viewer interface. But I am 
wondering how I could get the gene sequences based on gene symbol more 
efficiently and make it suitable to be commited by a script 
automatically. That is a very common task when dealing with the genome 
data. I bet there is a good solution already. I hope to get your suggestion.


Thank you in advance.


Chunlei Wu
Cancer Genomic Lab
MD Anderson Cancer Center



--__--__--

Message: 2
Date: 16 Jul 2002 04:04:04 -0000
From: "rajeshwar  gongalla" <bio100 at rediffmail.com>
To: bio_bulletin_board at bioinformatics.org 
Cc: "Chunlei Wu" <newgene at bigfoot.com>
Subject: Re: [BiO BB] How to get the gene sequence efficiently
Reply-To: bio_bulletin_board at bioinformatics.org 

Hai,
      What I understand from your query is to batch entries. which 
is option avaliable in entrez. what all u need to do is make text 
file of list of entries and submit as batch. If your question is 
different, please let me know. or else if you want to retrieve 
 from a genome with different key words try to write a perl 
program with patteren matching it will do the rest of work.

with regards,
G.RAJESHWAR
SCIENTIST-C
FRONTIER LIFE SCIENCE LTD.


On Tue, 16 Jul 2002 Chunlei Wu wrote :
>Hi, group,
>             I have a problem need the help from the group; it 
>may be easy for the experienced experts here.
>             I want to get the gene sequences for a list of genes 
>(with gene symbol, refseq accession number, etc). I know how to 
>get the gene sequence one-by-one from NCBI's genome viewer 
>interface. But I am wondering how I could get the gene sequences 
>based on gene symbol more efficiently and make it suitable to be 
>commited by a script automatically. That is a very common task 
>when dealing with the genome data. I bet there is a good solution 
>already. I hope to get your suggestion.
>
>
>Thank you in advance.
>
>
>Chunlei Wu
>Cancer Genomic Lab
>MD Anderson Cancer Center
>
>
>_______________________________________________
>BiO_Bulletin_Board maillist  -  
>BiO_Bulletin_Board at bioinformatics.org 
>http://bioinformatics.org/mailman/listinfo/bio_bulletin_board 

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--__--__--

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