[Biopython] <q> Bio Motif

[Lapointe, David]

Thanks Michiel,

I was assuming the replies went back to the list. Sorry.
________________________________________
From: Michiel de Hoon [mjldehoon at yahoo.com]
Sent: Saturday, January 07, 2012 9:54 AM
To: Lapointe, David
Subject: RE: [Biopython] <q> Bio Motif

Hi David,

It's better to reply to the list rather than to individual people. As a case in point, whereas I wrote some parts of Bio.Motif, I did not write the parts that you are using. My suggestion would be to cite "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by Richard Durbin et al. as a general reference for these kinds of analysis, but the actual author of the relevant parts of Bio.Motif may have other suggestions. I would also encourage you to cite the generic Biopython reference (PubMed ID 19304878).

Best,
-Michiel.

--- On Sat, 1/7/12, Lapointe, David <David.Lapointe at umassmed.edu> wrote:

> From: Lapointe, David <David.Lapointe at umassmed.edu>
> Subject: RE: [Biopython] <q> Bio Motif
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Date: Saturday, January 7, 2012, 9:05 AM
> Yes I should have been more specific.
> Not the third party parts ( MEME, etc). I am
> going   from a list of sequences, creating a
> PWM, then using the generated PWM to parse longer sequences
> for motifs. Mostly I am interested in information about the
> thresholds and interpreting results from search_pwm, but
> also some way to cite the method for publication.
>
> David
> ________________________________________
> From: Michiel de Hoon [mjldehoon at yahoo.com]
> Sent: Friday, January 06, 2012 10:49 PM
> To: biopython at lists.open-bio.org;
> Lapointe, David
> Subject: Re: [Biopython] <q> Bio Motif
>
> Which part of Bio.Motif are you using? Bio.Motif has
> various capabilities (parsing, PWM score calculation,
> threshold calculation), and different references may be
> applicable depending on how you are using Bio.Motif.
>
> -Michiel.
>
> --- On Fri, 1/6/12, Lapointe, David <David.Lapointe at umassmed.edu>
> wrote:
>
> > From: Lapointe, David <David.Lapointe at umassmed.edu>
> > Subject: [Biopython] <q> Bio Motif
> > To: "biopython at lists.open-bio.org"
> <biopython at lists.open-bio.org>
> > Date: Friday, January 6, 2012, 2:43 PM
> > Is there a reference to the algorithm
> > behind this module?
> >
> > David
> >
> > --
> > David Lapointe, Ph.D.
> > Director Scientific Computing/Information Services
> > University of Massachusetts Medical School
> > 55 Lake Avenue N
> > Worcester MA 01655
> > 508-856-5141 (v)
> > ' the lyf so short, the craft so long to lerne'
> >
> >
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>
>