2.1 Coevolution matrix

Step 1: Generating coevolution matrix

dyno_1_coevolution.py is a wrapper script: it does two things:

-Calls hhblits and hhfilter to generate a multiple sequence alignment (label.aln ) file which contains sequences of homologous proteins by searching through pre-clustered sequencences in the Uniref database. -runs CCMpred on the (label.aln ) to generate the coevolution matrix (.mat file) from the alignment. Ideally GPU is preferred for this step.

input arguments:

-f FASTA, --fasta standard fasta file. for sample file, check DyNoPy/test/001/1btl.fasta
-l LABEL, --label LABEL Label to be used for all output files. Appropriate file extensions will be added for each file.
-d DATABASE, --database DATABASEUniprot/Swiss prot protein sequence database label
-n NUMTHREADS, --numthreads NUMTHREADS number of threads to use for hh-blits. For CCMpred GPU is best. Code will check if GPU hardware is available and will decide to use either CPU or GPU for CCMpred

sample usage:

dyno_1_coevolution.py -i 1btl.fasta -n 12 -l 1btl