Multiple sequence alignment of 12 species

Question

i need to perform MSA( multiple sequence alignment on nucleotide sequences of 12 wheat varieties. all these varieties have different length bps(base pairs).I followed this documentation of MATLAB http://www.mathworks.in/help/bioinfo/ref/multialign.html. But when i type this "

ma = multialign(p53,tree,'ScoringMatrix',...
                {'pam150','pam200','pam250'})
showalignment(ma)"

i get an error :

??? Out of memory. Type HELP MEMORY for
your options.

Error in ==> profalign>affinegap at 648
F =  zeros(n+1,m+1,numStates);

Error in ==> profalign at 426
    [F, pointer] =
    affinegap(prof1,len1,prof2,len2,SM,go1,go2,ge1,ge2,wg1,wg2);

Error in ==> multialign at 655
    [profs{rootInd} h1 h2] =
    profalign(profs{[i,rootInd]},...

Please help

Can't replicate. Out of memory just means out of memory. If you're just following the documentation example it shouldn't happen, normally. Do you have a lot of other variables in your workspace? — nkjt, Aug 12 '14 at 09:11
Out of memory. `zeros(n+1,m+1,numStates)` this matrix is too large for your PC to hold in memory. — Yvon, Aug 14 '14 at 04:34
so what should i do so that my machine holds the distance matrix. so how to do alignment of 12 wheat varieties — user3395676, Aug 14 '14 at 06:48

score 0 · Answer 1 · answered Oct 01 '14 at 01:48

This is a hard problem to debug, because it is highly dependent on your specific settings. As mentioned in the comments, Matlab is saying that it ran out of memory. This might be because of the way you have Matlab configured or because your computer doesn't have enough RAM (or maybe you were using too much RAM for other things at the time). It's also possible that you just gave it more data than it can handle. However, assuming that the sequences aren't unreasonably long, 12 sequences should be pretty manageable for a progressive alignment algorithm, which multalign seems to be.

Given all of those variables, the simplest solution is just to avoid trying to run it on your computer. There are websites where you can submit your data to be aligned on a server that will definitely have sufficient RAM. The most popular of such websites is ClustalOmega, the successor to ClustalW. These sites will generally return results fairly quickly.

Multiple sequence alignment of 12 species

1 Answers1