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ASR by amino acid site-specific and asymmetric matrix (Read 2100 times)
Miguel AB
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Curious HyPhy user

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Madrid, Spain
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ASR by amino acid site-specific and asymmetric matrix
Apr 22nd, 2014 at 11:15am
 
Hi,

In our lab are very interesting in to perform ancestral sequence reconstruction (ASR) of amino acid sequences by using an "asymmetric" matrix (20x20) for each site. Cheesy
In the attachment you can find an example for a protein of 255 amino acids.  Smiley
We are wondering if we can work on a batchfile of Hyphy and try to implement this, do you think is this possible?. If yes, which batch file do you recommend to start working with?  Undecided

Many thanks!

All the best,
Miguel  Cheesy
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Miguel
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Hi Hyphy!

Posts: 53
CBMSO, CSIC (Spain)
Gender: male
Re: ASR by amino acid site-specific and asymmetric matrix
Reply #1 - Apr 22nd, 2014 at 1:15pm
 
Hi again,

I have been working on an batch file and I made some progress but still I need some help  Embarrassed
Attached you can find my batch files and an example, just run "RunMe_AA_ASR_2014.bf".  It will perform an ASR using the WAG model for all sites.

I am trying to specify a 20x20 asymmetric matrix for the model but the line "Model Mo = (matrix, Freqs, 1);" generated errors. Then, I need to specify this defined model into the ASR computation, I am not sure how can I do this.
Finally, I have to specify a matrix per site. One option is perform ASR per site, get an output file per site and finally somehow concatenate the info from all output files. I am wondering if there is a more simple fashion to do this.

Many thanks!  Cheesy
Miguel
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Miguel
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Hi Hyphy!

Posts: 53
CBMSO, CSIC (Spain)
Gender: male
Re: ASR by amino acid site-specific and asymmetric matrix
Reply #2 - Apr 23rd, 2014 at 6:50pm
 
Hi,

I've been trying to make progress on this, see attachment. Now I have specified the asymmetric matrix into a batch file that is called from the main batch file (just by following the procedure used for empirical amino acid models).
Apparently, it works well with an asymmetric matrix.  Cheesy

My questions are:
- What is the order of aa states in the 20x20 matrix and the freqs vector?, I mean, for example position 0 which aa state is?, and so on for the 20 (just need to know the aa letters behind the numbers..). I did not find this info in the manual of Hyphy.
- There is a paramter "t" in the matrix that I guess should be used to normalize the matrix but I do not know from where is it coming and which value should take.
- Finally, I could apply this script to perform ASR per site, generate an ASR file per site, and then concatenate all those files. But I am wondering if there is another way to do this easier and more elegant..
Many thanks!  Roll Eyes

Best,
Miguel
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