This is the command hmm-assembler.pl 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
hmm-assembler.pl - SNAP module hmm-assembler.pl
SYNOPSIS
hmm-assembler.pl [-OPTIONS [-MORE_OPTIONS]] [--] [PROGRAM_ARG1 ...]
OPTIONS
The following single-character options are accepted:
With arguments: -i -e -A -D -M -S -C -I -N -a -3 -5 -Z -c
Boolean (without arguments): -r -o -x -p -t -1
Options may be merged together. -- stops processing of options. Space is not required
between options and their arguments.
Options:
-i <length> [500]
-e <length> [1000]
-A <order:length> [0:30]
-D <order:length> [0:9]
-M <order:length> [0:15]
-S <order:length> [0:9]
-C <order> [4]
-I <order> [4]
-N <order> [4]
-3 <order:length> [] include 3'UTR model, requires -a
-a <order:length> [] include PolyA model, requires -3
-5 <order:length> [] include 5'UTR moel, requires -p
-p include generic promoter model, requires -5
-r include generic repeat model
-o include reverse ORF model
-x use explicit duration intron model
-t include C.elegans trans-splicing, requires -p, -5
-Z <clade> sets clade-specific values (worm, fly, plant)
-1 single gene model
-c <score>
include GC-AG splice donor model
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