This is the command positionDB that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
positionDB - management of posDB files
SYNOPSIS
positionDB [-mersize k] [-merskip k] [-use a-b,c] [-merbegin b] [-merend e] -sequence
s.fasta -output p.posDB
positionDB -dump datafile
positionDB -test1 sequence.fasta
positionDB -test2 db.fasta sequence.fasta
OPTIONS
Building an image
-mersize k
The size of the mers, default=20.
-merskip k
The skip between mers, default=0
-use a-b,c
Specify which sequences to use, default=all
-merbegin b
Build on a subset of the mers, starting at mer #b, default=all mers
-merend e
Build on a subset of the mers, ending at mer #e, default=all mers
-sequence s.fasta
Input sequences.
-output p.posDB
Output filename.
Dumping information about an image
-dump datafile.posDB
Running sanity tests
-test1 sequence.fasta
Tests if each and every mer is found in the positionDB. Reports if it doesn't find
a mer at the correct position. Doesn't report if table has too much stuff.
-test2 db.fasta sequence.fasta
Builds a positionDB from db.fasta, then searches the table for each mer in
sequence.fasta. Reports all mers it finds.
This is a silly test and you shouldn't do it.
Use positionDB online using onworks.net services
