[Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from PAML package)

Ryan Golhar golharam at umdnj.edu
Sat Jun 24 23:05:41 EDT 2006


>>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



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