hmm-assembler.pl(1)
SNAP module hmm-assembler.pl
Description
HMM-ASSEMBLER.PL
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:
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-i |
<length> [500] |
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-e |
<length> [1000] |
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-A |
<order:length> [0:30] |
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-D |
<order:length> [0:9] |
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-M |
<order:length> [0:15] |
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-S |
<order:length> [0:9] |
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-C |
<order> [4] |
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-I |
<order> [4] |
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-N |
<order> [4] |
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-3 |
<order:length> [] include 3’UTR model, requires -a |
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-a |
<order:length> [] include PolyA model, requires -3 |
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-5 |
<order:length> [] include 5’UTR moel, requires -p |
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-p |
include generic promoter model, requires -5 |
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-r |
include generic repeat model |
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-o |
include reverse ORF model |
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-x |
use explicit duration intron model |
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-t |
include C.elegans trans-splicing, requires -p, -5 |
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-Z |
<clade> sets clade-specific values (worm, fly, plant) |
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-1 |
single gene model |
-c <score>
include GC-AG splice donor model