[BiO BB] How to get the gene sequence efficiently

hz5 at njit.edu hz5 at njit.edu
Sat Sep 7 18:24:31 EDT 2002

Hi, Wu, 
Entrez has a batch retrieval tool that can be downloaded and run locally with a 
net connection.

If ou want to retrieve Drosophila or yeast, please go to flybase and SGD 
accordingly. They allow you to specify coordinate for your sequence. Ensemble 
does a better job in giving flanking sequence for human genes. but hard to 
specify coordinates.

I have a tool that retrieve any region of a specific human gene sequence. You 
give gene name, coordinates, it retrieve the sequence for you from NCBI. It 
allows batch retrieval. Like somebody has just retrieved upstream 20kb for 20 
sequences, just paste all the gene names, and give coordinate as from "-20000" 
to "-1", click and wait.

Hope this is helpful.
Haibo Zhang
Computational Biology, NJIT & Rutgers University
Quoting Chunlei Wu <newgene at bigfoot.com>:

> 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
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