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/Psi-BLAST> default=big_80 --db_h <database HHblits> default=uniprot20 --iter_p <number of iterations Psi-BLAST> default=2 (in this script) --iter_h <number of iterations HHblits,[1,8]> default=2 --eval_p <E-Value cutoff for Psi-BLAST, [0,1]> default=0.002 --eval_h <E-Value cutoff for HHblits, [0,1]> default=0.001 --c <checkpoins Psi-BLAST file name> ckeckpoint PSSM file should be created to search in other iterations (in other database) --r <checkpoins Psi-BLAST file name> ckeckpoint PSSM file to be reused to search in other iterations (in other database) --h prints this usage