[Bioperl-l] How to download EST files via bioperl script?

Alexander Kozik akozik at atgc.org
Mon Jul 9 08:25:14 EDT 2007


To download genomic sequences or ESTs for any organism (in various 
formats) you can use NCBI Taxonomy Browser:
http://www.ncbi.nlm.nih.gov/Taxonomy/

you can use taxonomy id to access different organisms, Arabidopsis for 
example (3702):
http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide&cmd=Search&dopt=DocSum&term=txid3702

or by direct web link:
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=Arabidopsis+thaliana&lvl=0&srchmode=1

assembled genomes can be accessed via ftp:
ftp://ftp.ncbi.nih.gov/genomes/

To download large amount of selected sequences (ESTs for example) you 
can use batch Entrez:
http://www.ncbi.nlm.nih.gov/entrez/query/static/advancedentrez.html
http://www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi?db=Nucleotide
(select EST for EST, it's critical)

It seems, to solve the problem you describe, you don't need to use 
bioperl. NCBI GenBank Entrez provides all necessary tools to work on 
these simple and frequent tasks.

-Alex

-- 
Alexander Kozik
Bioinformatics Specialist
Genome and Biomedical Sciences Facility
451 East Health Sciences Drive
University of California
Davis, CA 95616-8816
Phone: (530) 754-9127
email#1: akozik at atgc.org
email#2: akozik at gmail.com
web: http://www.atgc.org/



Xing Hu wrote:
> Hi friends,
> 
>     I wrote a script for getting genomic sequence file from GenBank. To 
> fulfill that target, I used DB::GenBank module to get the sequence via 
> get_Seq_by_acc, and it works well. But this time, facing enormous amount 
> of ESTs, I have no idea how to download them swiftly and elegantly.
> 
>     PROBLEM DESCRIPTION:
>     goal: download all EST files of a specific species from GenBank, say 
> Arabidopsis Thaliana or Oryza sativa(rice).
>     other: whether all of ESTs are in a single file or separatedly 
> placed does not matter.
> 
>     Can I use a bioperl script to achieve that? And How? I really 
> appreciate.
> 
> Xing.
> 
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