annotate augustus.xml @ 0:af307d3285c5 draft

Uploaded
author bgruening
date Sat, 06 Jul 2013 10:07:41 -0400
parents
children e2b822d7408f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
1 <tool id="augustus" name="Augustus" version="0.3">
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
2 <description>gene prediction for eukaryotic genomes</description>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
3 <requirements>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
4 <requirement type="package" version="2.7">augustus</requirement>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
5 <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
6 </requirements>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
7 <command>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
8 ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
9 ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
10 ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external script is used to extract the sequences into additional files
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
11
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
12 augustus
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
13 --strand=$strand
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
14 $noInFrameStop
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
15 $gff
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
16 $protein
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
17 $introns
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
18 $start
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
19 $stop
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
20 $cds
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
21 $codingseq
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
22 $singlestrand
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
23 $input_genome
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
24 $mea
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
25 $utr
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
26 --genemodel=$genemodel
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
27 --species=$organism
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
28 ##--outfile=$output
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
29 | tee $output
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
30 #if $protein or $codingseq:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
31 | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
32 #if $protein:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
33 --protein $protein_output
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
34 #end if
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
35 #if $codingseq:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
36 --codingseq $codingseq_output
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
37 #end if
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
38 #end if
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
39 </command>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
40 <inputs>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
41 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
42 <param name="noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons (--noInFrameStop)" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" help="Otherwise, intron-spanning stop codons could occur" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
43 <param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands (--singlestrand)" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
44 <param name="mea" type="boolean" label="Using the maximum expected accuracy approach (--mea)" truevalue="--mea=1" falsevalue="" checked="false" help="MEA is an alternative decoding approach." />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
45 <param name="utr" type="boolean" label="Predict the untranslated regions in addition to the coding sequence (--UTR)" truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
46
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
47 <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
48 <option value="human">Homo sapiens</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
49 <option value="fly">Drosophila melanogaster</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
50 <option value="arabidopsis">Arabidopsis thaliana</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
51 <option value="brugia ">Brugia malayi</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
52 <option value="aedes">Aedes aegypti</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
53 <option value="tribolium2012">Tribolium castaneum</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
54 <option value="schistosoma">Schistosoma mansoni</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
55 <option value="tetrahymena">Tetrahymena thermophila</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
56 <option value="galdieria">Galdieria sulphuraria</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
57 <option value="maize">Zea mays</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
58 <option value="toxoplasma ">Toxoplasma gondii</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
59 <option value="caenorhabditis ">Caenorhabditis elegans</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
60 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
61 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
62 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
63 <option value="aspergillus_terreus">Aspergillus terreus</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
64 <option value="botrytis_cinerea ">Botrytis cinerea</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
65 <option value="candida_albicans ">Candida albicans</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
66 <option value="candida_guilliermondii ">Candida guilliermondii</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
67 <option value="candida_tropicalis ">Candida tropicalis</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
68 <option value="chaetomium_globosum">Chaetomium globosum</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
69 <option value="coccidioides_immitis ">Coccidioides immitis</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
70 <option value="coprinus ">Coprinus cinereus</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
71 <option value="coprinus_cinereus">Coprinus cinereus</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
72 <option value="cryptococcus_neoformans_gattii ">Cryptococcus neoformans gattii</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
73 <option value="cryptococcus_neoformans_neoformans_B ">Cryptococcus neoformans neoformans</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
74 <option value="cryptococcus_neoformans_neoformans_JEC21 ">Cryptococcus neoformans neoformans</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
75 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
76 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
77 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
78 <option value="fusarium_graminearum ">Fusarium graminearum</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
79 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
80 <option value="(histoplasma)">Histoplasma capsulatum</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
81 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
82 <option value="laccaria_bicolor ">Laccaria bicolor</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
83 <option value="lamprey">Petromyzon marinus</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
84 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
85 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
86 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
87 <option value="neurospora_crassa">Neurospora crassa</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
88 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
89 <option value="pichia_stipitis">Pichia stipitis</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
90 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
91 <option value="saccharomyces_cerevisiae_S288C ">Saccharomyces cerevisiae</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
92 <option value="saccharomyces_cerevisiae_rm11-1a_1 ">Saccharomyces cerevisiae</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
93 <option value="(saccharomyces)">Saccharomyces cerevisiae</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
94 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
95 <option value="trichinella">Trichinella spiralis</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
96 <option value="ustilago_maydis">Ustilago maydis</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
97 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
98 <option value="nasonia">Nasonia vitripennis</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
99 <option value="tomato">Solanum lycopersicum</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
100 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
101 <option value="amphimedon">Amphimedon queenslandica</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
102 <option value="pneumocystis">Pneumocystis jirovecii</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
103 <option value="chicken">Gallus gallus domesticus (chicken)</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
104 <option value="cacao">Theobroma cacao (cacao)</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
105 <option value="heliconius_melpomene1">Heliconius melpomene</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
106 <option value="xenoturbella">Xenoturbella</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
107 </param>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
108
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
109 <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand.">
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
110 <option value="both">both</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
111 <option value="forward">forward</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
112 <option value="backward">backward</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
113 </param>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
114
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
115 <param name="genemodel" label="Gene Model" type="select" multiple="false" format="text" help="Gene Model to predict, for more information please refere to the help.">
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
116 <option value="complete">complete</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
117 <option value="partial">partial</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
118 <option value="intronless">intronless</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
119 <option value="atleastone">atleastone</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
120 <option value="exactlyone">exactlyone</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
121 <option value="bacterium">bacterium (beta version)</option>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
122 </param>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
123
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
124 <param name="protein" type="boolean" label="Output predicted protein sequences (--protein)" truevalue="--protein=on" falsevalue="--protein=off" checked="true" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
125 <param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file (codingseq)" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="true" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
126 <param name="introns" type="boolean" label="Output predicted intron sequences (--introns)" truevalue="--introns=on" falsevalue="--introns=off" checked="false" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
127 <param name="start" type="boolean" label="Output predicted start codons (--start)" truevalue="--start=on" falsevalue="--start=off" checked="false" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
128 <param name="stop" type="boolean" label="Output predicted stop codons (--stop)" truevalue="--stop=on" falsevalue="--stop=off" checked="false" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
129 <param name="cds" type="boolean" label="Output CDS region (--cds)" truevalue="--cds=on" falsevalue="--cds=off" checked="true" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
130 <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
131
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
132 </inputs>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
133 <outputs>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
134 <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
135 <change_format>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
136 <when input="gff" value="--gff3=on" format="gff" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
137 </change_format>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
138 </data>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
139 <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
140 <filter>protein == True</filter>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
141 </data>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
142 <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
143 <filter>codingseq == True</filter>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
144 </data>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
145 </outputs>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
146 <tests>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
147 <test>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
148 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
149 <param name="organism" value="human" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
150 <param name="utr" value="--UTR=on" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
151 <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="2"/>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
152 </test>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
153 <test>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
154 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
155 <param name="organism" value="human" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
156 <param name="utr" value="--UTR=on" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
157 <param name="gff" value="--gff3=on" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
158 <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="2"/>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
159 </test>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
160 <test>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
161 <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
162 <param name="organism" value="arabidopsis" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
163 <param name="singlestrand" value="--singlestrand=true" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
164 <param name="mea" value="--mea=1" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
165 <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
166 </test>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
167 <test>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
168 <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
169 <param name="organism" value="human" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
170 <param name="protein" value="--protein=on" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
171 <param name="codingseq" value="--codingseq=on" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
172 <param name="introns" value="--introns=on" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
173 <param name="cds" value="--cds=on" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
174 <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
175 <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
176 <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
177 </test>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
178 </tests>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
179 <help>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
180
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
181 **What it does**
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
182
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
183 AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
184 It can be used as an ab initio program, which means it bases its prediction purely on the
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
185 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
186 such as EST, MS/MS, protein alignments and synthenic genomic alignments.
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
187
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
188 -----
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
189
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
190 **Parameters**
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
191
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
192 Gene Model::
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
193
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
194 partial : allow prediction of incomplete genes at the sequence boundaries (default)
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
195 intronless : only predict single-exon genes like in prokaryotes and some eukaryotes
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
196 complete : only predict complete genes
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
197 atleastone : predict at least one complete gene
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
198 exactlyone : predict exactly one complete gene
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
199
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
200
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
201
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
202 **Example**
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
203
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
204 Suppose you have the following DNA formatted sequences::
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
205
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
206 >Seq1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
207 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
208 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
209 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
210 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
211 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
212
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
213 Running this tool will produce this::
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
214
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
215 # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
216 #
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
217 # Constraints/Hints:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
218 # (none)
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
219 # Predicted genes for sequence number 1 on both strands
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
220 # start gene g1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
221 scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
222 scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
223 scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
224 scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
225 scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
226 scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
227 scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
228 scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
229 scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
230 scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
231 scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
232 scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
233 scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
234 scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
235 scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
236
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
237
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
238 **References**
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
239
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
240 Mario Stanke and Stephan Waack (2003)
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
241 Gene Prediction with a Hidden-Markov Model and a new Intron Submodel.
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
242 Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
243
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
244
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
245 </help>
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
246 </tool>