SNAP module



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.


<length> [500]
<length> [1000]
<order:length> [0:30]
<order:length> [0:9]
<order:length> [0:15]
<order:length> [0:9]
<order> [4]
<order> [4]
<order> [4]
<order:length> [] include 3'UTR model, requires -a
<order:length> [] include PolyA model, requires -3
<order:length> [] include 5'UTR moel, requires -p
include generic promoter model, requires -5
include generic repeat model
include reverse ORF model
use explicit duration intron model
include C.elegans trans-splicing, requires -p, -5
<clade> sets clade-specific values (worm, fly, plant)
single gene model
-c <score>
include GC-AG splice donor model