This is the command mpialign 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
mpialign - parallel local alignment of biological sequences
SYNOPSIS
mpialign [-s scores] [-S split] [-H hblk] [-V vblk] file1 file2
DESCRIPTION
mpiAlign is a local sequence aligner, especially intended for use with large biological
DNA sequences, with more than 1Mbp (Millions of base pairs). It uses the Smith-Waterman
exact algorithm with affine gap cost function to perform this task.
General options:
-h display this help and exit
-s <scores>
specify a comma-separated list of scores to be used while calculating aligment
matrices throughout the program. The list must be in the format
"-sMATCH,MISMATCH,GAP_OPEN,GAP_EXTENSION" (without quotes), and is parsed in this
PRECISE order; no spaces are allowed between values. If there are any unspecified
parameters, these are set to default values and a warning message is issued;
exceeding parameters are discarded
Stage 2 options:
-S <split>
(mpialign only) number of parts in which to split the alignment matrix; after this
step a cyclic block model is applied, subdividing each part equally between all
available nodes
-H <hblk>
(mpialign only) number of horizontal subdivisions made by each node to its
alignment submatrix; since this value defines block width, a good choice should
allow two full matrix lines to fit the processor's cache pages, improving algorithm
performance
-V <vblk>
(mpialign only) number of vertical subdivisions made by each node to its alignment
submatrix; this value directly affects the amount of internode communication and is
used ONLY if 'split' is set to 1, otherwise it is set to the number of available
nodes
Use mpialign online using onworks.net services
