[Bioperl-l] question about the PAML module in bioperl

Mark A. Jensen maj at fortinbras.us
Fri Jan 30 21:10:42 EST 2009


Davide-
Maybe have a look at Bio::Align::DNAStatistics for kska?-- 
MAJ
----- Original Message ----- 
From: "Jason Stajich" <jason at bioperl.org>
To: "Davide Cora'" <cora at to.infn.it>
Cc: "bioperl list" <bioperl-l at lists.open-bio.org>
Sent: Friday, January 30, 2009 8:43 PM
Subject: Re: [Bioperl-l] question about the PAML module in bioperl


>I think it is probably that PAML 4.2 is not supported - we have not  
> been able to keep up with the constant change in output format in  
> PAML's more recent versions.  If you go back to PAML 3 it should work.  
> You should also give bioperl 1.6 a try, although I'm not confident  
> that it will work right now.
> 
> A proper testing of many of PAML's use-case outputs and validation of  
> the parsing across multiple-versions of PAML is on the list of things  
> that need to be done, but I doubt it is something I'll have much time  
> for right now.
> 
> -jason
> 
> On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote:
> 
>>
>> Dear Dr. Stajich,
>>
>> I work in a bioinformatic group at the University of Torino, Italy,  
>> and I write to you this email regarding a problem with the PAML  
>> module in bioperl.
>>
>> My goal is to evaluate the Ka/Ks ratio for a group of sequences and,  
>> to this end, I found a very nice example perl code based on bioperl:
>>
>> http://www.bioperl.org/wiki/HOWTO:PAML
>>
>> I tried to implement the example, but, unfortunately, it doesn't  
>> work (see the attached script).
>>
>> In particular, it seems that the part of the code relative to the  
>> clustalw alignment procedure works properly, but the second part,  
>> relative to the PAML execution, always stops with the following  
>> message:
>>
>> ........
>> .........
>> ..........
>> Sequence:110     Score:1115
>> Sequence:42     Score:1468
>> Sequence:52     Score:1752
>> Sequence:96     Score:1495
>> Alignment Score -1235112
>> GCG-Alignment file created      [/tmp/BtFAMhn879/L0AkU4W1UJ]
>>
>> -------------------- WARNING ---------------------
>> MSG: There was an error - see error_string for the program output
>> ---------------------------------------------------
>> Can't call method "get_MLmatrix" on an undefined value at  
>> prova_KaKs_bioperl.pl line 78, <GEN2> line 1099.
>>
>> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system.
>>
>> Do yo have any suggestion to solve this issue ?
>>
>> Could you suggest me a way to obtain a working code that is able to  
>> perform such analysis ? Do you have a piece of running code to  
>> obtain the KaKs ratio for a group of sequences ?
>>
>> Thanks in advance for your help,
>>
>> Davide
>>
>>
>>
>>
>> ---------------------------------
>> Davide Cora', PhD
>> Department of Theoretical Physics
>> University of Torino
>> Via P. Giuria 1
>> 10125, Torino, Italy
>>
>> email: cora at to.infn.it
>> web: http://www.to.infn.it/~cora/
>> phone: +39 011 6707238
>> --------------------------------- 
>> <yeast_cDNA_Known_Known.txt><prova_KaKs_bioperl.pl>
> 
> Jason Stajich
> jason at bioperl.org
> 
> 
> 
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>


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