edu.rit.compbio.seq

Class FindProteinHyb

java.lang.Object

edu.rit.compbio.seq.FindProteinHyb

public class FindProteinHyb
extends java.lang.Object

Class FindProteinHyb 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. The worker does each individual alignment in parallel in multiple threads using class ProteinLocalAlignmentSmp.

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