[Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from PAML package)
Alisha Holloway
akholloway at ucdavis.edu
Mon Jun 26 04:15:16 UTC 2006
Hi Ryan & Jason,
Sorry I didn't get back to you sooner. I escaped the central valley
heat (108!) and went to the coast for the weekend. I do have a
script that will call baseml and then parse the results. Here it is
and, Ryan, I can show you how to retrieve other parts of the data as
well, but you may already know how to do this. I know it's ugly, I
got it working and didn't clean it up. Just let me know if you need
more info.
Alisha
At 11:05 PM -0400 6/24/06, Ryan Golhar wrote:
> >>they make no assumption about coding sequence,
>>>where do you get that impression
>
>I get that information from the 1.5 api docs:
>
>http://doc.bioperl.org/releases/bioperl-1.5.0-RC1/
>
>Its documented under the description section.
>
>Oh well, I have it coded and working...might as well use it.
>
>Ryan
>-----Original Message-----
>From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason
>Stajich
>Sent: Saturday, June 24, 2006 9:38 PM
>To: golharam at umdnj.edu
>Cc: bioperl-l at lists.open-bio.org; 'Alisha Holloway'
>Subject: Re: [Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from PAML
>package)
>
>
>they make no assumption about coding sequence,where do you get that
>impression. the ka,ks are for coding but the tamura/nei kimura,
>jukes-cantor are all for any type of sequence.
>
>the phylip and emboss are pretty straightforward IMHO - you give it
>an alignment and you get out a matrix of pairwise numbers....
>\
>but whatever makes sense to you - we are using the same methods as
>are in Li's book (that is where I took the equations from).
>-j
>On Jun 24, 2006, at 2:57 PM, Ryan Golhar wrote:
>
>> Hi Jason,
>>
>> It looks like DNAStatistics is only for coding sequences. I'm
>> trying to
>> calculate the Ks of exons and the K (or Ki) of introns. All the
>> methods
>> in bioperl are based on coding sequences. Only the PAUP package
>> (that
>> I've found) does non-coding sequences. I would have used it but you
>> need to pay for it and we don't have the funding to purchase much
>> at the
>> moment.
>>
>> I brielfy looked at PHYLIP and EMBOSS but it didn't look as
>> straight-forward as I was hoping it would be. Either that, or I was
>> getting fustrated looking for a simple solution.
>>
>> In the end, I found a molecular evolution book that talks about
>> several
>> methods used for non-coding sequences so I went ahead and implemented
>> them. They seem to work well.
>>
>> Ryan
>>
>>
>> -----Original Message-----
>> From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of
>> Jason
>> Stajich
>> Sent: Saturday, June 24, 2006 2:43 PM
>> To: golharam at umdnj.edu
>> Cc: bioperl-l at lists.open-bio.org; 'Alisha Holloway'
>> Subject: Re: [Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from
>> PAML
>> package)
>>
>>
>> You should look at the Align::DNAStatistics module if you just want
>> pairwise DNA distance. I put in several different distance methods.
>> Or you can use the distance methods implemented in PHYLIP or EMBOSS
>> programs -- I thought you wanted the somewhat more sophisticated ML
>> approaches that are implemented in PAML?
>>
>> --jason
>>
>> On Jun 24, 2006, at 10:43 AM, Ryan Golhar wrote:
>>
>>> I've managed to code three methods to calculate K into a perl script
>>> using the algorithms as described in "Molecular Evolution" by Wen-
>>> Hsuing
>>> Li. I'd be happy to contribute it as a script...
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of
>>> Jason
>>> Stajich
>>> Sent: Saturday, June 24, 2006 9:40 AM
>>> To: golharam at umdnj.edu
>>> Cc: bioperl-l at lists.open-bio.org list; Alisha Holloway
>>> Subject: Re: [Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from
>>> PAML
>>> package)
>>>
>>>
>>> baseml is not well-supported to my knowledge - I think I started with
>>> attempt to capture a small amount of the data in the file. There are
> >> some people who have made modifications to possible parse it in-house
>>> but I know of no submitted patches. Many of the knowledgeable
>>> people are probably at the evolution meetings this week.
>>>
>>> I have no idea about the full set of information in the report files
>>> without going back to the Yang papers first. It depends on how much
>>> of that information you really want to capture of just the
>>> substitution rates.
>>>
>>> I'm Ccing Alisha in case she has ideas/solutions from her drosophila
>>> work+PAML.
>>>
>>> -jason
>>> On Jun 22, 2006, at 5:05 PM, Ryan Golhar wrote:
>>>
>>>> Hi all,
>>>>
>>>> I'm trying to use Bio::Tools::Phylo::PAML to parse the results from
>>>> baseml in the PAML package to measure the distances of some non-
>>>> coding
>>>
>>>> regions.
>>>>
>>>> I started with the coding regions, and used the script
>>>> bp_pairwise_kaks.pl without much trouble. Now, I'm trying to do
>>>> something similar for non-coding regions. However, when I call
>>>> Bio::Tools::Phylo::PAML::Result->get_MLmatrix(), I'm getting 'undef'
>>>> meaning matrix was never defined.
>>>>
>>>> I wanted to find out if anyone on here has done this before or
>>>> knows a
>>>
>>>> way to measure substitution frequencies of non-coding regions with
>>>> the
>>>
>>>> PAML package. The documentation with PAML is sparse so I'm not
>>>> sure how
>>>> to interpret its output directly - that's why I'm using Bioperl.
>>>>
>>>> Hopefully someone can help me before I start digging into the
>>>> code...Thanks.
>>>>
>>>> Ryan
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> --
>>> Jason Stajich
>>> Duke University
>>> http://www.duke.edu/~jes12
>>>
>>
>> --
>> Jason Stajich
>> Duke University
>> http://www.duke.edu/~jes12
>>
>
>--
>Jason Stajich
>Duke University
>http://www.duke.edu/~jes12
--
Alisha Holloway
Postdoctoral Fellow
Section of Evolution & Ecology
3347 Storer Hall
University of California
Davis, CA 95616
530-754-9551 Office
512-297-3958 Cell
530-752-1449 Fax
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