How To Make A .Free Format Sequence Alignment File (For Matlab) ?

Question

[Pals]

Hello, could anyone guide me generating a .free format alignment file? I am using MATLAB for making sequence analysis using SCA toolbox developed by Ranganathan group http://www.hhmi.swmed.edu/Labs/rr/sca.html. As I am newbie to MATLAB, I preferred following the tutorial and adapting codes.

Thanks in advance.

Kisun

[zhongyingmo]

Hi Kisun,

I just get started to try this method. Have you find out how to generate the .free file? Would you please let me know? I have no experience with bioinfomatics so any suggestion would be great! Thank you so much!

Zhongying

[Mayank Boob]

Any update on this?
I am still unable to figure it out.

Answer 1

[Graslevy]

Hey, you can achieve this if you have the bioinformatics toolbox provided by mathworks. Also, try code examples from http://www.computational-genomics.net/case_studies/, I found them very helpful!

[Pals]

Thanks for the supporting material.

Answer 2

[saladi]

Old post, but for those who get here in the future, one alternative is to use the multialignread function in the bioinformatics toolbox with a ClustalW, GCG, or PHYLIP formatted alignment:

 [labels,seqs]=multialignread(filename);
 labels=char(labels);
 seqs=char(seqs);