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Methodology Questions >> How to >> ASR by amino acid site-specific and asymmetric matrix

Message started by Miguel AB on Apr 22nd, 2014 at 11:15am

Title: ASR by amino acid site-specific and asymmetric matrix
Post by Miguel AB on Apr 22nd, 2014 at 11:15am

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. :D
In the attachment you can find an example for a protein of 255 amino acids.  :)
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?  :-/

Many thanks!

All the best,
Miguel  :D
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=Rate_matrix.txt (515 KB | 1 )

Title: Re: ASR by amino acid site-specific and asymmetric matrix
Post by Miguel on 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  :-[
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!  :D

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=Files_ASR_aa_AsymmSiteSpecificMatrices.zip (9 KB | 0 )

Title: Re: ASR by amino acid site-specific and asymmetric matrix
Post by Miguel on Apr 23rd, 2014 at 6:50pm

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.  :D

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!  ::)


http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=Files.zip (7 KB | 2 )

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