annotate glimmer_w_icm.xml @ 2:b1ad88bbc5fa draft default tip

Uploaded
author bgruening
date Mon, 12 Aug 2013 11:55:07 -0400
parents 841357e0acbf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
841357e0acbf Uploaded
bgruening
parents:
diff changeset
1 <tool id="glimmer_knowlegde-based" name="Glimmer3" version="0.2">
841357e0acbf Uploaded
bgruening
parents:
diff changeset
2 <description>Predict ORFs in prokaryotic genomes (knowlegde-based)</description>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
3 <requirements>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
4 <requirement type="package" version="3.02b">glimmer</requirement>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
5 <requirement type="package" version="1.61">biopython</requirement>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
6 <requirement type="set_environment">GLIMMER_SCRIPT_PATH</requirement>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
7 </requirements>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
8 <command>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
9 #import tempfile, os
841357e0acbf Uploaded
bgruening
parents:
diff changeset
10 #set $temp = tempfile.NamedTemporaryFile( delete=False )
841357e0acbf Uploaded
bgruening
parents:
diff changeset
11 #silent $temp.close()
841357e0acbf Uploaded
bgruening
parents:
diff changeset
12 #set $temp = $temp.name
841357e0acbf Uploaded
bgruening
parents:
diff changeset
13
841357e0acbf Uploaded
bgruening
parents:
diff changeset
14 glimmer3
841357e0acbf Uploaded
bgruening
parents:
diff changeset
15 --max_olap $max_olap
841357e0acbf Uploaded
bgruening
parents:
diff changeset
16 --gene_len $gene_len
841357e0acbf Uploaded
bgruening
parents:
diff changeset
17 --threshold $threshold
841357e0acbf Uploaded
bgruening
parents:
diff changeset
18 #if float( str($gc_percent) ) > 0.0:
841357e0acbf Uploaded
bgruening
parents:
diff changeset
19 --gc_percent $gc_percent
841357e0acbf Uploaded
bgruening
parents:
diff changeset
20 #end if
841357e0acbf Uploaded
bgruening
parents:
diff changeset
21
841357e0acbf Uploaded
bgruening
parents:
diff changeset
22 #if $stop_codon_opts.stop_codon_opts_selector == "gb":
841357e0acbf Uploaded
bgruening
parents:
diff changeset
23 --trans_table "${stop_codon_opts.genbank_gencode}"
841357e0acbf Uploaded
bgruening
parents:
diff changeset
24 #else:
841357e0acbf Uploaded
bgruening
parents:
diff changeset
25 --stop_codons "${stop_codon_opts.stop_codons}"
841357e0acbf Uploaded
bgruening
parents:
diff changeset
26 #end if
841357e0acbf Uploaded
bgruening
parents:
diff changeset
27
841357e0acbf Uploaded
bgruening
parents:
diff changeset
28 --start_codons $start_codons
841357e0acbf Uploaded
bgruening
parents:
diff changeset
29
841357e0acbf Uploaded
bgruening
parents:
diff changeset
30 $linear
841357e0acbf Uploaded
bgruening
parents:
diff changeset
31 $no_indep
841357e0acbf Uploaded
bgruening
parents:
diff changeset
32 $extend
841357e0acbf Uploaded
bgruening
parents:
diff changeset
33 $seq_input
841357e0acbf Uploaded
bgruening
parents:
diff changeset
34 $icm_input
841357e0acbf Uploaded
bgruening
parents:
diff changeset
35 $temp 2>&#38;1;
841357e0acbf Uploaded
bgruening
parents:
diff changeset
36
841357e0acbf Uploaded
bgruening
parents:
diff changeset
37 ## convert prediction to FASTA sequences
841357e0acbf Uploaded
bgruening
parents:
diff changeset
38 \$GLIMMER_SCRIPT_PATH/glimmer2seq.py $temp".predict" $seq_input $genes_output;
841357e0acbf Uploaded
bgruening
parents:
diff changeset
39
841357e0acbf Uploaded
bgruening
parents:
diff changeset
40 #if $report:
841357e0acbf Uploaded
bgruening
parents:
diff changeset
41 mv $temp".predict" $report_output;
841357e0acbf Uploaded
bgruening
parents:
diff changeset
42 #else:
841357e0acbf Uploaded
bgruening
parents:
diff changeset
43 rm $temp".predict";
841357e0acbf Uploaded
bgruening
parents:
diff changeset
44 #end if
841357e0acbf Uploaded
bgruening
parents:
diff changeset
45
841357e0acbf Uploaded
bgruening
parents:
diff changeset
46 #if $detailed_report:
841357e0acbf Uploaded
bgruening
parents:
diff changeset
47 mv $temp".detail" $detailed_output;
841357e0acbf Uploaded
bgruening
parents:
diff changeset
48 #else:
841357e0acbf Uploaded
bgruening
parents:
diff changeset
49 rm $temp".detail";
841357e0acbf Uploaded
bgruening
parents:
diff changeset
50 #end if
841357e0acbf Uploaded
bgruening
parents:
diff changeset
51
841357e0acbf Uploaded
bgruening
parents:
diff changeset
52 rm $temp
841357e0acbf Uploaded
bgruening
parents:
diff changeset
53 </command>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
54 <inputs>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
55 <param name="seq_input" type="data" format="fasta" label="Genome Sequence" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
56 <param name="icm_input" type="data" format="data" label="Interpolated context model (ICM)" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
57
841357e0acbf Uploaded
bgruening
parents:
diff changeset
58 <param name="max_olap" type="integer" value="50" label="Set maximum overlap length" help="Overlaps this short or shorter are ignored." />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
59 <param name="gene_len" type="integer" value="90" label="Set the minimum gene length to n nucleotides" hrlp="This does not include the bases in the stop codon."/>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
60 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene" help="If the in-frame score >= N, then the region is given a number and considered a potential gene." />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
61 <param name="gc_percent" type="float" value="0.0" label="Set the GC percentage of the independent model, i.e., the model of intergenic sequence" help="If 0.0 specified, the GC percentage will be counted from the input file." />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
62
841357e0acbf Uploaded
bgruening
parents:
diff changeset
63 <param name="linear" type="boolean" truevalue="--linear" falsevalue="" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
64 <param name="no_indep" type="boolean" truevalue="--no_indep" falsevalue="" checked="false" label="Don’t use the independent probability score column at all" help="Using this option will produce more short gene predictions." />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
65 <param name="extend" type="boolean" truevalue="--extend" falsevalue="" checked="false" label="Also score orfs that extend off the end of the sequence(s)" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
66 <param name="start_codons" type="text" value="atg,gtg,ttg" label="Specify start codons as a comma-separated list" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
67
841357e0acbf Uploaded
bgruening
parents:
diff changeset
68 <conditional name="stop_codon_opts">
841357e0acbf Uploaded
bgruening
parents:
diff changeset
69 <param name="stop_codon_opts_selector" type="select" label="Specify start codons as">
841357e0acbf Uploaded
bgruening
parents:
diff changeset
70 <option value="gb" selected="True">Genbank translation table entry</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
71 <option value="free_form">Comma-separated list</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
72 </param>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
73 <when value="gb">
841357e0acbf Uploaded
bgruening
parents:
diff changeset
74 <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons">
841357e0acbf Uploaded
bgruening
parents:
diff changeset
75 <option value="1" select="True">1. Standard</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
76 <option value="2">2. Vertebrate Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
77 <option value="3">3. Yeast Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
78 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
79 <option value="5">5. Invertebrate Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
80 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
81 <option value="9">9. Echinoderm Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
82 <option value="10">10. Euplotid Nuclear</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
83 <option value="11">11. Bacteria and Archaea</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
84 <option value="12">12. Alternative Yeast Nuclear</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
85 <option value="13">13. Ascidian Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
86 <option value="14">14. Flatworm Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
87 <option value="15">15. Blepharisma Macronuclear</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
88 <option value="16">16. Chlorophycean Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
89 <option value="21">21. Trematode Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
90 <option value="22">22. Scenedesmus obliquus mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
91 <option value="23">23. Thraustochytrium Mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
92 <option value="24">24. Pterobranchia mitochondrial</option>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
93 </param>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
94 </when>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
95 <when value="free_form">
841357e0acbf Uploaded
bgruening
parents:
diff changeset
96 <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
97 </when>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
98 </conditional>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
99
841357e0acbf Uploaded
bgruening
parents:
diff changeset
100 <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output"/>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
101 <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file"/>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
102 </inputs>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
103 <outputs>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
104 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
105 <data name="report_output" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
841357e0acbf Uploaded
bgruening
parents:
diff changeset
106 <filter>report == True</filter>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
107 </data>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
108 <data name="detailed_output" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
841357e0acbf Uploaded
bgruening
parents:
diff changeset
109 <filter>detailed_report == True</filter>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
110 </data>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
111 </outputs>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
112 <tests>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
113 <test>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
114 <param name="seq_input" value='streptomyces_Tu6071_genomic.fasta' />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
115 <param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
116 <param name="max_olap" value="50" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
117 <param name="gene_len" value="90" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
118 <param name="threshold" value="30" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
119 <param name="gc_percent" value="0.0" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
120 <param name="linear" value="--linear" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
121 <param name="no_indep" value="" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
122 <param name="extend" value="" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
123 <param name="start_codons" value="atg,gtg,ttg" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
124 <param name="genbank_gencode" value="11" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
125 <param name="detailed_report" value="" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
126 <param name="report" value="" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
127 <output name="genes_output" file='glimmer_w_icm_trans-table-11_genomic.fasta' ftype="fasta" />
841357e0acbf Uploaded
bgruening
parents:
diff changeset
128 </test>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
129 </tests>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
130 <help>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
131
841357e0acbf Uploaded
bgruening
parents:
diff changeset
132
841357e0acbf Uploaded
bgruening
parents:
diff changeset
133 **What it does**
841357e0acbf Uploaded
bgruening
parents:
diff changeset
134
841357e0acbf Uploaded
bgruening
parents:
diff changeset
135 This is the main program that makes gene preditions based on an interpolated context model (ICM).
841357e0acbf Uploaded
bgruening
parents:
diff changeset
136
841357e0acbf Uploaded
bgruening
parents:
diff changeset
137 The ICM can be generated with extracted CDS from related organisms (ICM builder). If you can't generate an ICM model you can use the non knowlegde-based Glimmer with a de novo prediction.
841357e0acbf Uploaded
bgruening
parents:
diff changeset
138
841357e0acbf Uploaded
bgruening
parents:
diff changeset
139 -----
841357e0acbf Uploaded
bgruening
parents:
diff changeset
140
841357e0acbf Uploaded
bgruening
parents:
diff changeset
141 **Example**
841357e0acbf Uploaded
bgruening
parents:
diff changeset
142
841357e0acbf Uploaded
bgruening
parents:
diff changeset
143 *Input*::
841357e0acbf Uploaded
bgruening
parents:
diff changeset
144
841357e0acbf Uploaded
bgruening
parents:
diff changeset
145 - interpolated context model (ICM): Use the 'Glimmer ICM builder' tool to create one
841357e0acbf Uploaded
bgruening
parents:
diff changeset
146 - Genome Sequence in FASTA format
841357e0acbf Uploaded
bgruening
parents:
diff changeset
147
841357e0acbf Uploaded
bgruening
parents:
diff changeset
148 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
841357e0acbf Uploaded
bgruening
parents:
diff changeset
149 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
841357e0acbf Uploaded
bgruening
parents:
diff changeset
150 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
841357e0acbf Uploaded
bgruening
parents:
diff changeset
151 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
841357e0acbf Uploaded
bgruening
parents:
diff changeset
152 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
841357e0acbf Uploaded
bgruening
parents:
diff changeset
153 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
841357e0acbf Uploaded
bgruening
parents:
diff changeset
154 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
841357e0acbf Uploaded
bgruening
parents:
diff changeset
155 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
841357e0acbf Uploaded
bgruening
parents:
diff changeset
156 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
841357e0acbf Uploaded
bgruening
parents:
diff changeset
157 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
841357e0acbf Uploaded
bgruening
parents:
diff changeset
158 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
841357e0acbf Uploaded
bgruening
parents:
diff changeset
159 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
841357e0acbf Uploaded
bgruening
parents:
diff changeset
160 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
841357e0acbf Uploaded
bgruening
parents:
diff changeset
161 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
841357e0acbf Uploaded
bgruening
parents:
diff changeset
162 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
841357e0acbf Uploaded
bgruening
parents:
diff changeset
163 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
841357e0acbf Uploaded
bgruening
parents:
diff changeset
164 .....
841357e0acbf Uploaded
bgruening
parents:
diff changeset
165
841357e0acbf Uploaded
bgruening
parents:
diff changeset
166 *Output*::
841357e0acbf Uploaded
bgruening
parents:
diff changeset
167
841357e0acbf Uploaded
bgruening
parents:
diff changeset
168 - FASTA file with predicted proteins
841357e0acbf Uploaded
bgruening
parents:
diff changeset
169 - Glimmer prediction file (optional)
841357e0acbf Uploaded
bgruening
parents:
diff changeset
170
841357e0acbf Uploaded
bgruening
parents:
diff changeset
171 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7.
841357e0acbf Uploaded
bgruening
parents:
diff changeset
172 orf00001 40137 52 +2 8.68
841357e0acbf Uploaded
bgruening
parents:
diff changeset
173 orf00004 603 34 -1 2.91
841357e0acbf Uploaded
bgruening
parents:
diff changeset
174 orf00006 1289 1095 -3 3.16
841357e0acbf Uploaded
bgruening
parents:
diff changeset
175 orf00007 1555 1391 -2 2.33
841357e0acbf Uploaded
bgruening
parents:
diff changeset
176 orf00008 1809 1576 -1 1.02
841357e0acbf Uploaded
bgruening
parents:
diff changeset
177 orf00010 1953 2066 +3 3.09
841357e0acbf Uploaded
bgruening
parents:
diff changeset
178 orf00011 2182 2304 +1 0.89
841357e0acbf Uploaded
bgruening
parents:
diff changeset
179 orf00013 2390 2521 +2 0.60
841357e0acbf Uploaded
bgruening
parents:
diff changeset
180 orf00018 2570 3073 +2 2.54
841357e0acbf Uploaded
bgruening
parents:
diff changeset
181 orf00020 3196 3747 +1 2.91
841357e0acbf Uploaded
bgruening
parents:
diff changeset
182 orf00022 3758 4000 +2 0.83
841357e0acbf Uploaded
bgruening
parents:
diff changeset
183 orf00023 4399 4157 -2 1.31
841357e0acbf Uploaded
bgruening
parents:
diff changeset
184 orf00025 4463 4759 +2 2.92
841357e0acbf Uploaded
bgruening
parents:
diff changeset
185 orf00026 4878 5111 +3 0.78
841357e0acbf Uploaded
bgruening
parents:
diff changeset
186 orf00027 5468 5166 -3 1.64
841357e0acbf Uploaded
bgruening
parents:
diff changeset
187 orf00029 5590 5832 +1 0.29
841357e0acbf Uploaded
bgruening
parents:
diff changeset
188 orf00032 6023 6226 +2 6.02
841357e0acbf Uploaded
bgruening
parents:
diff changeset
189 orf00033 6217 6336 +1 3.09
841357e0acbf Uploaded
bgruening
parents:
diff changeset
190 ........
841357e0acbf Uploaded
bgruening
parents:
diff changeset
191
841357e0acbf Uploaded
bgruening
parents:
diff changeset
192 - Glimmer detailed report (optional)
841357e0acbf Uploaded
bgruening
parents:
diff changeset
193
841357e0acbf Uploaded
bgruening
parents:
diff changeset
194 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7.
841357e0acbf Uploaded
bgruening
parents:
diff changeset
195 Sequence length = 40222
841357e0acbf Uploaded
bgruening
parents:
diff changeset
196
841357e0acbf Uploaded
bgruening
parents:
diff changeset
197 ----- Start ----- --- Length ---- ------------- Scores -------------
841357e0acbf Uploaded
bgruening
parents:
diff changeset
198 ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC
841357e0acbf Uploaded
bgruening
parents:
diff changeset
199 0001 +2 40137 40137 52 135 135 9.26 96 - 96 - - 3 - 0
841357e0acbf Uploaded
bgruening
parents:
diff changeset
200 0002 +1 58 64 180 120 114 5.01 69 69 - - 30 - - 0
841357e0acbf Uploaded
bgruening
parents:
diff changeset
201 +3 300 309 422 120 111 -0.68 20 - - 20 38 - - 41
841357e0acbf Uploaded
bgruening
parents:
diff changeset
202 +3 423 432 545 120 111 1.29 21 - 51 21 13 - 8 5
841357e0acbf Uploaded
bgruening
parents:
diff changeset
203 0003 +2 401 416 595 192 177 2.51 93 - 93 - 5 - - 1
841357e0acbf Uploaded
bgruening
parents:
diff changeset
204 0004 -1 645 552 34 609 516 2.33 99 - - - 99 - - 0
841357e0acbf Uploaded
bgruening
parents:
diff changeset
205 +1 562 592 762 198 168 -2.54 1 1 - - - - - 98
841357e0acbf Uploaded
bgruening
parents:
diff changeset
206 +1 763 772 915 150 141 -1.34 1 1 - - - - 86 11
841357e0acbf Uploaded
bgruening
parents:
diff changeset
207 +3 837 846 1007 168 159 1.35 28 - 50 28 - - 17 3
841357e0acbf Uploaded
bgruening
parents:
diff changeset
208 0005 -3 1073 977 654 417 321 0.52 84 - - - - - 84 15
841357e0acbf Uploaded
bgruening
parents:
diff changeset
209 0006 -3 1373 1319 1095 276 222 3.80 99 - - - - - 99 0
841357e0acbf Uploaded
bgruening
parents:
diff changeset
210 0007 -2 1585 1555 1391 192 162 2.70 98 - - - - 98 - 1
841357e0acbf Uploaded
bgruening
parents:
diff changeset
211 0008 -1 1812 1809 1576 234 231 1.26 94 - - - 94 - - 5
841357e0acbf Uploaded
bgruening
parents:
diff changeset
212 0009 +2 1721 1730 1945 222 213 0.68 80 - 80 - - - - 19
841357e0acbf Uploaded
bgruening
parents:
diff changeset
213 .....
841357e0acbf Uploaded
bgruening
parents:
diff changeset
214
841357e0acbf Uploaded
bgruening
parents:
diff changeset
215 -------
841357e0acbf Uploaded
bgruening
parents:
diff changeset
216
841357e0acbf Uploaded
bgruening
parents:
diff changeset
217 **References**
841357e0acbf Uploaded
bgruening
parents:
diff changeset
218
841357e0acbf Uploaded
bgruening
parents:
diff changeset
219 A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).
841357e0acbf Uploaded
bgruening
parents:
diff changeset
220
841357e0acbf Uploaded
bgruening
parents:
diff changeset
221
841357e0acbf Uploaded
bgruening
parents:
diff changeset
222 </help>
841357e0acbf Uploaded
bgruening
parents:
diff changeset
223
841357e0acbf Uploaded
bgruening
parents:
diff changeset
224 </tool>