edu.rit.compbio.seq

Class FindProteinHyb2

java.lang.Object

edu.rit.compbio.seq.FindProteinHyb2

public class FindProteinHyb2
extends java.lang.Object

Class FindProteinHyb2 is a hybrid parallel program that finds matches for a protein in a protein sequence database. The query sequence is stored in a file in FASTA format; for further information, see class ProteinSequence. The protein sequence database is stored in two files, a database file in FASTA format and an index file; for further information, see class ProteinDatabase. The program uses the Smith-Waterman algorithm to compute a local alignment between the query sequence and each subject sequence in the database. The program uses the BLOSUM-62 protein substitution matrix. The program uses affine gap penalties with a gap existence penalty of −11 and a gap extension penalty of −1. The program prints on the standard output the resulting alignments from highest to lowest score. The program only prints alignments with an E-value below the given threshold; if not specified, the default is 10.

The program uses the master-worker pattern for load balancing. The program partitions the alignments among the processes using the schedule specified by the -Dpj.schedule flag. The master sends a range of database indexes to a worker; the worker sends back to the master a list of alignments for those database indexes; and the process repeats. Within each worker, the alignments are partitioned among multiple threads using the parallel loop schedule specified by the fourth command line argument. If this argument is missing, the default is to divide the alignments evenly among the threads.

Usage: java -Dpj.np=Kp -Dpj.nt=Kt [ -Dpj.schedule=procschedule ] edu.rit.compbio.seq.FindProteinHyb2 queryfile databasefile indexfile [ thrschedule [ expect ] ]
Kp = Number of parallel processes
Kt = Number of parallel threads per process
procschedule = Load balancing schedule for processes (default: fixed schedule)
queryfile = Query sequence file
databasefile = Protein sequence database file
indexfile = Protein sequence index file
thrschedule = Load balancing schedule for threads (default: fixed schedule)
expect = E-value threshold (default: 10)

Method Summary

Modifier and Type	Method and Description
static void	main(java.lang.String[] args) Main program.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Main program.

Throws:

java.lang.Exception