[Biopython-dev] Primary Sequence of all protein (help)

[Rodrigo Faccioli]

Peter,

Thank you for your reply.

Actually, we want to store the sequence of the fasta files in a relational
database which has been developed by my research group. So, we have
developed some calculations with primary sequence of proteins.

We did not download the PDB database because our computation of protein
properties are based on their primary sequence. Therefore, our idea is to
work with the primary sequence of all proteins. My understanding is the PDB
database contains the proteins which is known their tearty structure. The
others are in other database.

Thanks in advance,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


On Tue, Mar 16, 2010 at 4:42 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Tue, Mar 16, 2010 at 7:24 PM, Rodrigo Faccioli
> <rodrigo_faccioli at uol.com.br> wrote:
> >
> > Hi all,
> >
> > I want to know the primary sequence (fasta file) of all proteins. In
> other
> > the words, I would like a database which contain the fasta files of all
> > proteins.
> >
> > I'm a computer scientist and I don't know how hard it is. However, we
> have
> > worked with SEQRES section of PDB files and BioPython. So, we want to
> work
> > with fasta files and BioPython to check our results.
>
> A single FASTA file of all know proteins would be enormous. Even the
> non-redundant ("nr") dataset used by the NCBI for their hugely popular
> BLAST search is pretty big.
>
> It sounds like many all you need is a FASTA file containing all the
> sequences with structures in the PDB - something you may be
> able to download directly from the PDB FTP site.
>
> Peter
>