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How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
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15 months ago
Nari • 870
United States

I have over 1000 files each having 30 sequences. Manually aligning, removing stop codons and then calculating avarage dN/dS for each file is impossible for me.
Are there ways to perform this via command drive.
(I know PAML, but no tool known for aligning in paml format and for removing stop codons)
Even 3 different tools for each step will do, the thing is just that I should be able to do it from command prompt.

(I'm on Win7)

Thanks in advance.

paml • 8.1k views
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what aligner would you like to use? Most, if not all, have a command line. Deleting the stop codons afterwards should be "trivial". E.g. biopython has an interface for most aligners and will run PAML as well. However, please keep in mind that dN/dS calculations are (obviously) very dependent on a good alignment. The huge downside of this automated approach will be that you will likely not quality check each alignment before moving on.

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Hello, I have a similar problem?In big data,I must delete the stop codons in the sequence.So,can you give me some suggestions?

Thanks!

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24 months ago
jprmachado • 60

Hi,

Few time ago i got the same problem. I solved using a perl script available here (https://gist.github.com/josephhughes/1167776). Since is needed to feed with both nuclotides and amino acids i have used t-coffee to translate.

This have worked fine for me. I have done in linux, for windows you may neeed to write a .bat file to it easily. Take a look on bat files tutorial for syntax if you are not familiar with that. I think that will work.

You can use fasta format as sequence file for PAML no need of .pml format.

Regards,

Joao

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Thanks so much!!

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Hi @jprmachado

I am working dn/ds for 4431 gene clusters, i tried to remove stopcodons by pal2nal program. but for some reason around 198 cultures still has the stop codons.

now i have tried to remove the stopcodons with the above script but i don't get any error and stop codons are not removed.

any suggestions thank you

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3.2 years ago
SES 8.2k
Vancouver, BC

Pal2Nal will generate a codon alignment without stop codons, given a MSA of proteins and the corresponding DNA sequences. If the input is a pairwise alignment, I believe it will calculate dN/dS ratios (using PAML) for you automatically. Otherwise, you can just input your alignments to PAML to calculate dN/dS. Pal2Nal is written in Perl, so it should work on your Win7 machine (I don't know about PAML though, unless there is a Windows version available).

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should the nucleotide alignment be trimmed? And also the protein alignment be trimmed?

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