[Biopython] PSI-BLAST help

Sat Jan 2 07:27:27 UTC 2010

I have a problem in database search using PSI-BLAST.
I have to do PSI-BLAST against combined "nr" and "environmental
sequences(env_nr)" databases.
I need to iterate 10 rounds.
Web services allow selecting one database at a time.

Do Biopython offers search against multiple databases.
I am unable to find any simple way to do this.

Regards,
Alaguraj.V

On 12/29/09, biopython-request at lists.open-bio.org <
biopython-request at lists.open-bio.org> wrote:
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> Today's Topics:
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>    1. Re: Superpose structures... DONE (Michiel de Hoon)
>    2. Remove hydrogens... (Yasser Almeida Hern?ndez)
>    3. Comparison between bioperl and biopython? (Peng Yu)
>    4. Re: [Bioperl-l] Comparison between bioperl and    biopython?
>       (Jason Stajich)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 28 Dec 2009 09:27:23 -0800 (PST)
> From: Michiel de Hoon <mjldehoon at yahoo.com>
> Subject: Re: [Biopython] Superpose structures... DONE
> To: BioPython <biopython at biopython.org>, almeida at cim.sld.cu
> Message-ID: <363342.11278.qm at web62406.mail.re1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> --- On Mon, 12/28/09, Yasser Almeida Hern?ndez <pedro.al at fenhi.uh.cu>
> wrote:
> > Now i have another question. It is possible in Biopython
> > read gziped pdb files (.pdb.gz)?
>
> I am not a Bio.PDB user, but from its documentation it looks like it uses
> the file name to open a PDB file instead of a handle. Thomas, how do you
> feel about modifying Bio.PDB so it uses a file handle instead of a file
> name? Then Bio.PDB can parse gzipped and bzipped files.
>
> --Michiel.
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 29 Dec 2009 09:18:38 -0500
> From: Yasser Almeida Hern?ndez <pedro.al at fenhi.uh.cu>
> Subject: [Biopython] Remove hydrogens...
> To: BioPython <biopython at biopython.org>
> Message-ID: <20091229091838.fnyk66sayos8swww at correo.fenhi.uh.cu>
> Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
>         format="flowed"
>
> Hi all...
> How can i remove hydrogens atoms from the structures objects?
>
> Thanks
>
> --
> Lic. Yasser Almeida Hern?ndez
> Center of Molecular Inmunology (CIM)
> Nanobiology Group
> P.O.Box 16040, Havana, Cuba
> Phone: (537) 271-7933, ext. 221
>
> ----------------------------------------------------------------
> Correo FENHI
>
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 29 Dec 2009 10:08:09 -0600
> From: Peng Yu <pengyu.ut at gmail.com>
> Subject: [Biopython] Comparison between bioperl and biopython?
> To: bioperl-l at lists.open-bio.org, biopython at lists.open-bio.org
> Message-ID:
>         <366c6f340912290808q6edea4d8ncb59a270f9d11f1a at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> May I ask somebody who are versitile in both bioperl and biopython
> comment on the pros and cons of bioperl and biopython? I'm sending
> this email to both bioperl and biopython mailing lists. But I hope
> that it will not result in any contention.
>
> I assume that the functionality between bioperl or biopython is the
> same, i.e., tasks can be done in bioperl can be done biopython and
> vice versa, as both libraries have been out there over 10 years.
> Please correct me if my understanding is not true.
>
> Given that a task that can be done with either bioperl or biopython,
> I, in particularly, want to know how long it will take to write the
> code for the task in bioperl and biopython, with the same readability
> requirement (see below) and the assumption that users have the same
> fluency in perl and python.
>
> python is claimed to be good for maintainability. But perl is
> criticized for there-are-many-ways-for-a-given-task. Since there are
> multiple ways in perl, let us assume that we always use perl in a
> readable way.
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 29 Dec 2009 08:49:20 -0800
> From: Jason Stajich <jason at bioperl.org>
> Subject: Re: [Biopython] [Bioperl-l] Comparison between bioperl and
>         biopython?
> To: Peng Yu <pengyu.ut at gmail.com>
> Cc: bioperl-l at lists.open-bio.org, biopython at lists.open-bio.org
> Message-ID: <2B85EF86-8A84-491B-8C33-7EC16CCB8CBC at bioperl.org>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Are you asking for the purposes of choosing a toolkit for your work or
> just curious about the advantages/disadvantages of language choice?
>
> -jason
> On Dec 29, 2009, at 8:08 AM, Peng Yu wrote:
>
> > May I ask somebody who are versitile in both bioperl and biopython
> > comment on the pros and cons of bioperl and biopython? I'm sending
> > this email to both bioperl and biopython mailing lists. But I hope
> > that it will not result in any contention.
> >
> > I assume that the functionality between bioperl or biopython is the
> > same, i.e., tasks can be done in bioperl can be done biopython and
> > vice versa, as both libraries have been out there over 10 years.
> > Please correct me if my understanding is not true.
> >
> > Given that a task that can be done with either bioperl or biopython,
> > I, in particularly, want to know how long it will take to write the
> > code for the task in bioperl and biopython, with the same readability
> > requirement (see below) and the assumption that users have the same
> > fluency in perl and python.
> >
> > python is claimed to be good for maintainability. But perl is
> > criticized for there-are-many-ways-for-a-given-task. Since there are
> > multiple ways in perl, let us assume that we always use perl in a
> > readable way.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> http://fungalgenomes.org/
>
>
>
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> End of Biopython Digest, Vol 84, Issue 32
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