[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
Entrez has a batch retrieval tool that can be downloaded and run locally with a
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
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.
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
> Thank you in advance.
> Chunlei Wu
> Cancer Genomic Lab
> MD Anderson Cancer Center
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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