Question: How To Make A .Free Format Sequence Alignment File (For Matlab) ?
0
gravatar for Pals
8.8 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

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

sequence analysis matlab • 3.8k views
ADD COMMENTlink modified 2.8 years ago by saladi130 • written 8.8 years ago by Pals1.3k

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

ADD REPLYlink written 8.0 years ago by zhongyingmo0

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

ADD REPLYlink written 5.8 years ago by Mayank Boob0
1
gravatar for Graslevy
8.8 years ago by
Graslevy240
UK
Graslevy240 wrote:

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!

ADD COMMENTlink modified 10 months ago by RamRS28k • written 8.8 years ago by Graslevy240

Thanks for the supporting material.

ADD REPLYlink written 8.8 years ago by Pals1.3k
0
gravatar for saladi1
2.8 years ago by
saladi130
United States
saladi130 wrote:

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);
ADD COMMENTlink modified 10 months ago by RamRS28k • written 2.8 years ago by saladi130
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