[Bioperl-l] program bp_pairwise_kaks

Jason Stajich jason at bioperl.org
Thu Jan 22 18:55:24 UTC 2009

Markus -

i'm confused about what you want to get out at the end.

Do you want is a good alignment at the codon level for coding  
sequences but you want to align in protein space?

To do  this:
  There are several bits of code in the pairwise_kaks script that you  
can use as a starting palce but you don't need to codeml if you don't  
want to calculate ka and ks values.
Basically you translate to protein, align in protein space, and remap  
back to codons.  There are several functions in bioperl that help do  
all of this - the pairwise_kaks script is a good example of how to  
write such a script but you may need to modify it for your own needs.

Please keep your emails to the mailing list as well it helps others  
chime in if they have answers and also allows people to look back and  
see solutions if they have similar problems.

On Jan 22, 2009, at 7:30 AM, Markus Liebscher wrote:

> Hi Jason,
> to explain a little bit what I want to do. I know you could be of  
> valuable help with this. I have a plenty of sequences that have a  
> diverge origin in both protein family and species. But what I want  
> to have is an alignment of all sequences against each another on  
> preferable DNA level and than do codon optimization having the  
> degenerate code (regardless of organism) to improve the alignment  
> score to a maximum.
> Do you think this program is of any help for this or do you have  
> another idea what program I can use for this?
> Again thanks a lot,
> Markus.
> Jason Stajich wrote:
>> Markus-
>> You need to have also installed PAML in order to do the calculation  
>> with PAML.  There is example code on the HOWTOs for running the  
>> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics
>> Jason Stajich
>> jason at bioperl.org <mailto:jason at bioperl.org>
>> http://bioperl.org/wiki/User:Jason
>> ---------- Forwarded message ----------
>> From: *Markus Liebscher* <Markus.Liebscher at gmx.de <mailto:Markus.Liebscher at gmx.de 
>> >>
>> Date: Tue, Jan 20, 2009 at 6:22 AM
>> Subject: program bp_pairwise_kaks
>> To: jason at bioperl.org <mailto:jason at bioperl.org>
>> Dear Jason,
>> I found the Bioperl package very useful. But I failed to run the  
>> bp_pairwise_kaks program.
>> I tried to run bp_pairwise_kaks as suggested using the command line  
>> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna.
>> The program starts the routine but at the end I get this:
>> --------------------------------------------------------
>> CLUSTAL W (1.82) Multiple Sequence Alignments
>> Sequence format is Pearson
>> Sequence 1: CBG10100        363 aa
>> Sequence 2: F22B7.13        525 aa
>> Sequence 3: C38C10.4        525 aa
>> Start of Pairwise alignments
>> Aligning...
>> Sequences (1:2) Aligned. Score:  9
>> Sequences (1:3) Aligned. Score:  8
>> Sequences (2:3) Aligned. Score:  96
>> Guide tree        file created:   [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd]
>> Start of Multiple Alignment
>> There are 2 groups
>> Aligning...
>> Group 1: Sequences:   2      Score:11215
>> Group 2:                     Delayed
>> Sequence:1     Score:2745
>> Alignment Score 3187
>> GCG-Alignment file created      [/tmp/5M8igBfS6R/JI0anpGzWn]
>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty  
>> at /usr/lib/perl5/site_perl/5.10/Bi
>> o/Tools/Run/WrapperBase.pm line 243
>> SEQ1    SEQ2    Ka      Ks      Ka/Ks   PROT_PERCENTID   
>> --------------------------------------------------------
>> Do you have an idea what happened here and how I can solve this  
>> problem? I appreciate any help with this.
>> I am running Cygwin under Windows XP, and have installed clustalw,  
>> t-coffee, the bioperl package and the bioperl package run with the  
>> "Build" scripts.
>> Best regards,
>> Markus.
>> Dr. Markus Liebscher
>> Martin-Luther-University Halle/Wittenberg
>> Dept. Natural product chemistry
>> Kurt-Mothes-Str.3
>> 06120 Halle (Saale)
>> Germany

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