[Bioperl-l] load sequence files into Mysql

[Hilmar Lapp]

Li, you might want to consider to subscribe to the Bulletin Board at 
bioinformatics.org. The genbank database is at 
ftp://ftp.ncbi.nih.gov/genbank. gbest*.seq.gz is the EST database.

It is not segregated by species, but it is easy to screen out by 
species using the --seqfilter option of load_seqdatabase.pl.

	-hilmar

On Dec 11, 2005, at 5:29 PM, chen li wrote:

> Hi Hilmar,
>
> Thanks for the replay.
>
> Do you mean the files in this link:
>
> ftp://ftp.ncbi.nih.gov/repository/dbEST/
>
> There are many files out in this folder. I am not sure
> which one belongs to mouse.
>
>
> Li
>
> --- Hilmar Lapp <hlapp at gmx.net> wrote:
>
>> Have you tried the GenBank EST database flat files
>> (in GenBank format)?
>>
>> On Dec 11, 2005, at 12:47 PM, chen li wrote:
>>
>>> Hi all,
>>>
>>> I already install Biosql on my computer and
>> everything
>>> works fine. Now I want to download some mouse EST
>>> database files which can be read into mysql
>> correctly
>>> without anymore modifications. Where can I
>> download
>>> these files or other sequence files?  And I know
>> it
>>> still has some problems to read the fasta files
>> from
>>> NCBI(as Hilmar already points out). The link
>> provided
>>> in the HOWTO is broken.
>>>
>>> Any suggestion will be appreciated and thanks in
>>> advance.
>>>
>>>
>>>
>>> Li
>>>
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>>
> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp
>> at gnf.org
>> GNF, San Diego, Ca. 92121              phone:
>> +1-858-812-1757
>>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------