← Back to branch summary

~ubuntu-branches/debian/jessie/ugene/jessie

« back to all changes in this revision

Viewing changes to data/workflow_samples/Transcriptomics/SearchTFBS.uwl

  • Committer: Package Import Robot
  • Author(s): Steffen Moeller
  • Date: 2011-11-02 13:29:07 UTC
  • mfrom: (1.2.1) (3.1.11 natty)
  • Revision ID: package-import@ubuntu.com-20111102132907-o34gwnt0uj5g6hen
Tags: 1.9.8+repack-1
* First release to Debian
  - added README.Debian
  - increased policy version to 3.9.2
  - added URLs for version control system
* Added debug package.

Show diffs side-by-side

added added

removed removed

Lines of Context:
data/workflow_samples/Transcriptomics/SearchTFBS.uwl
 
1
#!UGENE_WORKFLOW
 
2
#Predicts binding sites for number of transcription factors of interest using SITECON algorithm.The present workflow sample is designed for simultaneous recognition of binding sites for 3 different transcription factor types, you can expand it for recognition of any desired number of transription factor types.SITECON - is a program pakage for recognition of potential transcription factor binding sites basing on the data about conservative conformational and physicochemical properties revealed on the basis of the binding sites sets analysis.Citing SITECON        Please cite:Oshchepkov D.Y., Vityaev E.E., Grigorovich D.A., Ignatieva E.V., Khlebodarova T.M.SITECON:a tool for detecting conservative conformational and physicochemicalproperties in transcription factor binding site alignments and for siterecognition. // Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W208-12.
 
3
 
 
4
workflow "Search for transcription factor binding sites ( TFBS) in genomic sequences"{
 
5
 
 
6
    read-sequence {
 
7
        type:read-sequence;
 
8
        name:"Read sequence";
 
9
        merge-gap:10;
 
10
        mode:0;
 
11
    }
 
12
    sitecon-search {
 
13
        type:sitecon-search;
 
14
        name:"Search for TFBS with SITECON";
 
15
        err1:0;
 
16
        err2:0.001;
 
17
        min-score:85;
 
18
        result-name:misc_feature;
 
19
        strand:0;
 
20
    }
 
21
    sitecon-search2 {
 
22
        type:sitecon-search;
 
23
        name:"Search for TFBS with SITECON 2";
 
24
        err1:0;
 
25
        err2:0.001;
 
26
        min-score:85;
 
27
        result-name:misc_feature;
 
28
        strand:0;
 
29
    }
 
30
    sitecon-search3 {
 
31
        type:sitecon-search;
 
32
        name:"Search for TFBS with SITECON 3";
 
33
        err1:0;
 
34
        err2:0.001;
 
35
        min-score:85;
 
36
        result-name:misc_feature;
 
37
        strand:0;
 
38
    }
 
39
    write-genbank {
 
40
        type:write-genbank;
 
41
        name:"Write Genbank";
 
42
        accumulate:true;
 
43
        write-mode:2;
 
44
    }
 
45
    sitecon-read {
 
46
        type:sitecon-read;
 
47
        name:"Read SITECON model";
 
48
    }
 
49
    sitecon-read2 {
 
50
        type:sitecon-read;
 
51
        name:"Read SITECON model 2";
 
52
    }
 
53
    sitecon-read3 {
 
54
        type:sitecon-read;
 
55
        name:"Read SITECON model 3";
 
56
    }
 
57
 
 
58
    read-sequence.sequence->sitecon-search.in-sequence.sequence
 
59
    sitecon-read.sitecon-model->sitecon-search.in-sitecon.sitecon-model
 
60
    read-sequence.sequence->sitecon-search2.in-sequence.sequence
 
61
    sitecon-read2.sitecon-model->sitecon-search2.in-sitecon.sitecon-model
 
62
    read-sequence.sequence->sitecon-search3.in-sequence.sequence
 
63
    sitecon-read3.sitecon-model->sitecon-search3.in-sitecon.sitecon-model
 
64
    sitecon-search3.annotations->write-genbank.in-sequence.annotations
 
65
    read-sequence.annotations->write-genbank.in-sequence.annotations
 
66
    sitecon-search.annotations->write-genbank.in-sequence.annotations
 
67
    sitecon-search2.annotations->write-genbank.in-sequence.annotations
 
68
    read-sequence.sequence->write-genbank.in-sequence.sequence
 
69
 
 
70
    .meta {
 
71
        visual {
 
72
            read-sequence {
 
73
                tooltip:"Reads sequences and annotations if any from local or remote files.";
 
74
                pos:"-795 -585";
 
75
                style:simple;
 
76
                bg-color-ext:"0 128 128 64";
 
77
                out-sequence.angle:360;
 
78
            }
 
79
            sitecon-search {
 
80
                tooltip:"Searches each input sequence for transcription factor binding sites significantly similar to specified SITECON profiles. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations for each sequence.";
 
81
                pos:"-630 -585";
 
82
                style:simple;
 
83
                bg-color-ext:"0 128 128 64";
 
84
                in-sequence.angle:183.18;
 
85
                in-sitecon.angle:273.814;
 
86
                out-annotations.angle:360;
 
87
            }
 
88
            sitecon-search2 {
 
89
                tooltip:"Searches each input sequence for transcription factor binding sites significantly similar to specified SITECON profiles. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations for each sequence.";
 
90
                pos:"-510 -585";
 
91
                style:simple;
 
92
                bg-color-ext:"0 128 128 64";
 
93
                in-sequence.angle:183.576;
 
94
                in-sitecon.angle:273.576;
 
95
                out-annotations.angle:360;
 
96
            }
 
97
            sitecon-search3 {
 
98
                tooltip:"Searches each input sequence for transcription factor binding sites significantly similar to specified SITECON profiles. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations for each sequence.";
 
99
                pos:"-390 -585";
 
100
                style:simple;
 
101
                bg-color-ext:"0 128 128 64";
 
102
                in-sequence.angle:178.21;
 
103
                in-sitecon.angle:271.364;
 
104
                out-annotations.angle:360;
 
105
            }
 
106
            write-genbank {
 
107
                tooltip:"Writes all supplied sequences and related annotations to file(s) in Genbank format.";
 
108
                pos:"-240 -585";
 
109
                style:simple;
 
110
                bg-color-ext:"0 128 128 64";
 
111
                in-sequence.angle:180;
 
112
            }
 
113
            read-sequence.out-sequence->sitecon-search.in-sequence {
 
114
                text-pos:"-27.5 -24";
 
115
            }
 
116
            sitecon-search.out-annotations->sitecon-search2.in-sequence {
 
117
                text-pos:"-45 -37";
 
118
            }
 
119
            sitecon-search2.out-annotations->sitecon-search3.in-sequence {
 
120
                text-pos:"-45 -37";
 
121
            }
 
122
            sitecon-read {
 
123
                tooltip:"Reads SITECON profiles from file(s). The files can be local or Internet URLs.";
 
124
                pos:"-630 -465";
 
125
                style:simple;
 
126
                bg-color-ext:"0 128 128 64";
 
127
                out-sitecon.angle:88.727;
 
128
            }
 
129
            sitecon-read2 {
 
130
                tooltip:"Reads SITECON profiles from file(s). The files can be local or Internet URLs.";
 
131
                pos:"-510 -465";
 
132
                style:simple;
 
133
                bg-color-ext:"0 128 128 64";
 
134
                out-sitecon.angle:85.486;
 
135
            }
 
136
            sitecon-read3 {
 
137
                tooltip:"Reads SITECON profiles from file(s). The files can be local or Internet URLs.";
 
138
                pos:"-390 -465";
 
139
                style:simple;
 
140
                bg-color-ext:"0 128 128 64";
 
141
                out-sitecon.angle:90;
 
142
            }
 
143
            sitecon-read.out-sitecon->sitecon-search.in-sitecon {
 
144
                text-pos:"-37 -24";
 
145
            }
 
146
            sitecon-read2.out-sitecon->sitecon-search2.in-sitecon {
 
147
                text-pos:"-37 -24";
 
148
            }
 
149
            sitecon-read3.out-sitecon->sitecon-search3.in-sitecon {
 
150
                text-pos:"-37 -24";
 
151
            }
 
152
            sitecon-search3.out-annotations->write-genbank.in-sequence {
 
153
                text-pos:"-45 -37";
 
154
            }
 
155
        }
 
156
    }
 
157
}
 
158