When I employ the "Sequence Alignment application" of Matlab on big size genes, I stop by an error regards to the matrix array size. That's why the requested array exceeds maximum array size preference. For instance, it goes to be an array of "300020x300020" which, needs 83.8GB of RAM in order to process!
Is there any alternative solution able to deal with this matter?
I do appreciate if someone can guide me!
You can try an alignment algorithm outside of Matlab e.g Emboss. Another way I use usually is to split the query sequence (the one I am trying to align) into chunks and do a local alignment one chunk at a time and combine them at the end.
Umar, thank you for the response. Actually, I've already tried Emboss but, it failed to process for some genes, for instance, CACNA!A . Can you guide how I can use it in my specific case? In the case of splitting approach, I do not know actually that how can I do that. It would be great if you can explain to me or give me an approach to deal with.
I am not close to a computer right now, I'll try and do it on Wednesday when I am back at a computer. I can look for some R code, its very similar to Matlab so may be straightforward
Hi Reza
I had a look through some of my code, the most recent code I could fine was something like this: see attached file.
The oSeqPred is an object that contains the long sequence, while oSeqIGHc is the smaller list of sequences (usually a gene split on exons). Then I align each locally and eventually combine them into a single matrix, that can be exported in a format of your choice.
I hope it helps. Or else I have to dig deeper to find even older code which depends on when I find the time.
Cheers
Umar
Thank you so much Umar1
I realised the logic of your suggestion, however, I am not familiar with R. I am gonna write it based on Matlab script. Anyway, it would be great if you can let me know other suitable solution in your convinient time. Cheers
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