[Bioperl-l] load sequence files into Mysql

[chen li]

Thanks all for the informatiom.

Li

--- Hilmar Lapp <hlapp at gmx.net> wrote:

> 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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> >>
> >>
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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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