Run.pl

run.pl=

Performs a BLAST/PSI-BLAST/HHblits run with custom parameters on biolab computers.

You can find the script run.pl here on biocluster: /mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1. The usage of the script with examples can also be found in the header of the file itself.

Usage: perl run.pl --in <input sequence file> --out_b <output blast file> --out_p <output psiblast file> --out_h <output hhblits file> [options]
--db_b <database blast/psiblast> default=big_80
--db_h <database hhblits> default=uniprot20
--iter_p <number of iterations psiblast> default=2 (in this script)
--iter_h <number of iterations hhblits,[1,8]> default=2
--c <checkpoins file name. ckeckpoint PSSM file should be created to search in other iterations (in other database)
--r <checkpoins file name. ckeckpoint PSSM file to be reused to search in other iterations (in other database)
--h prints this usage