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