edu.rit.compbio.seq

Class FindProteinSeq

java.lang.Object

edu.rit.compbio.seq.FindProteinSeq

public class FindProteinSeq
extends java.lang.Object

Class FindProteinSeq is a sequential 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 does all the alignments sequentially, in a single thread. The program uses class ProteinLocalAlignmentSeq to do the alignments.

Usage: java edu.rit.compbio.seq.FindProteinSeq queryfile databasefile indexfile [ expect ]
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