I am trying to calculate accuracy for my program which does prediction of aminoacid-aminoacid interactions. However, I am using ClustalW to create multiple sequence alignments, and it changes the input sequence,modifies it with adding gaps or other aminoacids. To be able to compare accuracy for the contact maps I created for my prediction and for the PDB file, they have to be in same size. At the moment, the matrix of PDB file is 70 and the one I predicted is 90. Do you have an idea of how to stop Clustalw to not to disturb the first sequence which is my input? I am using this code for Clustalw:
clustalw_cline = ClustalwCommandline("clustalw2", infile=name_to_align, outfile=filename, outorder= 'ALIGNED')
Also, I have changed the outorder to 'INPUT' but it did not change anything..
Any help would be appreciated,thank you.