Reply To: How to obtain alignment file for comparative modeling under Rosetta 3.1?

[Anonymous]

I solved it by myself, thanks for the open source.

For “general” alignment file format, it is unbelievable simple:

score nnn.nnn

queryID startPos seq

templID startPos seq

queryID startPos seq

templID startPos seq

–# for start another alignment

score nnn.nnn

queryID startPos seq

templID startPos seq

queryID startPos seq

templID startPos seq

I do not know which aligner generates this “general” file format. Then we need another utility to convert any other aligner’s output to this format. It seems Rosetta-CM calculates identities and gaps in its own code, although I think all the aligner will provide such information with the alignment result.

Anyway, thanks to the Rosetta contributors.

len