[Biopython] <q> Bio Motif

[Lapointe, David]

Thanks!
________________________________________
From: biopython-bounces at lists.open-bio.org [biopython-bounces at lists.open-bio.org] On Behalf Of Bartek Wilczynski [bartek at rezolwenta.eu.org]
Sent: Saturday, January 07, 2012 7:13 PM
To: Lapointe, David
Cc: biopython at lists.open-bio.org
Subject: Re: [Biopython] <q> Bio Motif

Hi David,

The references given by Michiel are fine. If you are using the
specific methods for choosing the thresholds based on the expected
false positive/negative rates you could cite the paper by Svedn
Rahmann et al. (pubmed id 16646785).

best Bartek

On Sat, Jan 7, 2012 at 11:39 PM, Lapointe, David
<David.Lapointe at umassmed.edu> wrote:
> 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'
>> >
>> >
>> > _______________________________________________
>> > Biopython mailing list  -  Biopython at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biopython
>> >
>>
>>
>
>
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--
Bartek Wilczynski

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