Java for MSA to compare two sequences from different files

Question

[nabilabidbensalem.2014]

Hi everybody

I have two MSA files 1 and 2. Each file contains 10 sequences from 1 to 10.

I'd like to compare sequence 1 (file 1) with sequence 1 (file 2), sequence 1 (file 1) with sequence 2 (file 2), sequence 1 (file 1) with sequence 3 (file 2)..........., sequence 1 (file 1) with sequence 10 (file 2).

then, the same for sequence 2 (file 1),.................., sequence 10 (file 1).

The same for sequences of the file 2.

Is there any java package that can do that job?

Thanks

[Brian Bushnell]

What do you mean by "compare"?

And are these amino acids or nucleotides?

[nabilabidbensalem.2014]

These are nucleotide sequences and I want to compare them but as matrix

[nabilabidbensalem.2014]

pair alignment

[nabilabidbensalem.2014]

nucleic acid sorry

Answer 1

[Brian Bushnell]

The BBMap package has a program called "idmatrix" that will generate the all-to-all identity values for a single fasta file:

idmatrix.txt in=file.fasta out=matrix.txt

The input has to be a normal fasta file, though, not a msa file with gaps ("-") mixed in with the bases.

[nabilabidbensalem.2014]

Thank you very much