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

Thanks a lot. I do appreciate any guidance you would do.

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