1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="Hacker Hands">
<META NAME="author" CONTENT="Josep F. Abril">
<!-- $Id: GFF2APLOT.html,v 1.9 2002/02/07 16:31:05 gmaster Exp gmaster $ -->
<META NAME="keywords" CONTENT="GFF2APLOT HOWTOs, tutorials, GFF, gff-format, Genomic Pairwise Alignments PostScript Plots, Genomic Analysis, Homology, Sinteny, Bioinformatics, SIM">
<META NAME="description" CONTENT="GFF2APLOT HOWTOs: Analyzing SIM output for a syntenic sequences pair.">
<TITLE>GFF2APLOT HOWTOs: SIM output for a syntenic sequences pair.</TITLE>
<!-- <BASE HREF="http://genome.imim.es/software/gfftools/gff2aplot_docs/mhcregion/"> -->
<link rel=stylesheet type="text/css" href="http://genome.imim.es/Genome.css" title="Genome">
<link rel=stylesheet type="text/css" href="http://genome.imim.es/software/gfftools/gff2aplot_docs/HowTo.css" title="Genome">
<STYLE type="text/css">
@import url(http://genome.imim.es/Genome_forms_mozilla.css);
</STYLE>
<SCRIPT type="text/javascript" src="http://genome.imim.es/Genome.js"></SCRIPT>
</head>
<body onResize="init();" MARGINWIDTH="2" MARGINHEIGHT="0">
<A NAME="TOP"></A>
<!-- ############### TITLE AREA ############### -->
<table border=0 cellpadding=0 cellspacing=0 width="100%">
<tr>
<td align="center">
<FONT size=4 class="tit">Genome BioInformatics Research Lab</FONT>
</td>
</tr>
</table>
<!-- ############### MENU AREA ############### -->
<table class="default" border=0 cellpadding=0 cellspacing=0 width="100%">
<tr>
<td class="links" align="CENTER">
<a href="http://genome.imim.es/main/help.html"
onMouseover="window.status='Asking for Help';">Help</a>
<FONT style="color: #005050;">|</FONT>
<a href="http://genome.imim.es/main/news.html"
onMouseover="window.status='News';">News</a>
<FONT style="color: #005050;">|</FONT>
<a href="http://genome.imim.es/main/people.html"
onMouseover="window.status='Who is who in Genome Informatics Research Laboratory';">People</a>
<FONT style="color: #005050;">|</FONT>
<a href="http://genome.imim.es/main/research.html"
onMouseover="window.status='Research at our Group';">Research</a>
<FONT style="background: #005050; color: #FFFFFF;">
<a href="http://genome.imim.es/main/software.html"
style="background: #005050; color: #DDDDDD;"
onMouseover="window.status='Software developed in our Group';">Software</a>
</FONT> <!-- Current menu -->
<a href="http://genome.imim.es/main/publications.html"
onMouseover="window.status='Publications by our Group';">Publications</a>
<FONT style="color: #005050;">|</FONT>
<a href="http://genome.imim.es/main/links.html"
onMouseover="window.status='Interesting Links';">Links</a>
</td>
</tr>
<tr>
<td class="links" align="CENTER">
<a href="http://genome.imim.es/main/databases.html"
onMouseover="window.status='Datasets created/curated by our Group';" class="hh">Resources & Datasets</a>
<FONT style="color: #005050;">|</FONT>
<a href="http://genome.imim.es/genepredictions/index.html"
onMouseover="window.status='Gene Predictions produced by our Software';" class="hh">Gene Predictions</a>
<FONT style="color: #005050;">|</FONT>
<a href="http://genome.imim.es/main/seminars.html"
onMouseover="window.status='Seminars, Courses and Group Sessions';" class="hh">Seminars & Courses</a>
</td>
</tr>
</table><BR class="hhh">
<!-- ############### PATH AREA ############### -->
<table border=1 cellpadding=0 cellspacing=0 width="100%">
<tr>
<td class="path" border=0 cellpadding=0 cellspacing=0 ALIGN="LEFT">
<table border=0 cellpadding=0 cellspacing=1>
<tr>
<td class="ppath" border=0 cellpadding=0 cellspacing=0>
<a href="http://www.imim.es/"
onMouseover="window.status='Institut Municipal d\'Investigació Mèdica';">IMIM</a>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<a href="http://www.upf.es/"
onMouseover="window.status='Universitat Pompeu Fabra';">UPF</a>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<a href="http://www.crg.es/"
onMouseover="window.status='Centre de Regulació Genòmica';">CRG</a>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<a href="http://www.imim.es/grib/eng/default.htm"
onMouseover="window.status='Grup de Recerca en Informtica Biomèdica';">GRIB</a>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<A HREF="http://genome.imim.es/index.html" onMouseover="window.status='Genome Informatics Research Laboratory HOME PAGE: You are Welcome!!!'">
<IMG SRC="http://genome.imim.es/g_icons/lhr.gif" ALT="HOME" HEIGHT=10 WIDTH=36 BORDER=0>
</A>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<a href="http://genome.imim.es/main/software.html"
onMouseover="window.status='Software';">SOFTWARE</a>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#TOP"
onMouseover="window.status='This is the main page for GFF2APLOT.';">gff2aplot</a>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<a href="http://genome.imim.es/software/gfftools/GFF2APLOT.html#HOWTOS"
onMouseover="window.status='GFF2APLOT Tutorials...';">HowTo</a>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<IMG SRC="http://genome.imim.es/g_icons/dmd.gif" ALT="*" HEIGHT=8 WIDTH=8 BORDER=0>
</td><td class="ppath" border=0 cellpadding=0 cellspacing=0>
<a href="http://genome.imim.es/software/gfftools/gff2aplot_docs/mhcregion/index.html#TOP"
onMouseover="window.status='An Alignment from WU-BLAST';">SIM Data</a>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ############### USERS AREA ############### -->
<table border=0 cellpadding=0 cellspacing=0 width="100%">
<tr border=0 cellpadding=0 cellspacing=0>
<td class="section" border=0 cellpadding=0 cellspacing=0 width="10px"> </td>
<td class="section" ALIGN=CENTER>
<CENTER><FONT size=6 class="tgen"> SIM Alignment on a Multigenic Syntenic Region </FONT></CENTER>
</td>
<td class="section" border=0 cellpadding=0 cellspacing=0 width="10px"> </td>
</tr>
<tr border=0 cellpadding=0 cellspacing=0>
<td class="userspace" border=0 cellpadding=0 cellspacing=0 width="10px"> </td>
<td class="userspace" border=0 cellpadding=0 cellspacing=0>
<BR>
<A NAME="TOC"></A>
<P>
<FONT size=5 class="K"> Summary </FONT> <BR class="kk"><BR>
We will visualize the output produced by SIM on the genomic MHC syntenic region between human and mouse. We will use a filter to convert its output into GFF, the C program <code>ali2gff</code> is included in the <code>gff2aplot</code> distribution. <BR>
Once we have generated the whole genomic region figure, we will zoom into a single gene annotation. This will illustrate how you can expand a given area from your pictures, to highlight single features on multigenic annotation plots for instance. <BR class="kk"><BR>
<B>NOTE.-</B> For the sake of clarity, we are going to use long names for the comand-line switches. See the command-line help if you prefer short names for those cases in which a short name is available. <BR>
Bitmaps for the examples were generated as PNGs (Portable Network Graphics). If your browser is not ready for such format yet, you can visualize the PDF or PS versions by clicking on the links below each snapshot. Links to customization files, log files, GFF input files and output PostScript figures, are also available on each command-line shown. <BR>
</P>
<P>
<FONT size=5 class="K"> Contents </FONT>
<UL>
<LI><A HREF="index.html#ALIGFF" onMouseover="window.status='GFF from SIM';">Translating SIM output into GFF.</A> <BR></LI>
<LI><A HREF="index.html#RAW" onMouseover="window.status='Raw output from GFF2APLOT';">Raw <code>gff2aplot</code> output.</A> <BR></LI>
<LI><A HREF="index.html#CUST" onMouseover="window.status='Whole genomic MHC region plot';">Finishing whole genomic region plot.</A> <BR></LI>
<LI><A HREF="index.html#ZOOM" onMouseover="window.status='Zooming into LMP2 gene region';">Zooming into single gene regions.</A> <BR></LI>
</UL> <BR class="hh">
</P>
<TABLE border=0 cellpadding=0 cellspacing=0 width="100%">
<TR>
<TD class="section" width=80% ALIGN=LEFT>
<a name="ALIGFF"></a><FONT size=5 class="K"> Parsing SIM Output </FONT>
</TD>
<TD class="section" width=20% ALIGN=RIGHT>
<a href="index.html#TOP"
onMouseover="window.status='TOP of the PAGE';">
<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
</TD></TR>
</TABLE>
<P> <BR class="hh">
</P>
<P><CENTER><TABLE class="userspace" border=0 cellpadding=0 cellspacing=0><TR><TD class="codebg"> </TD><TD class="codebg" ALIGN=LEFT> <BR class="hh"><PRE class="codefg">
$BIN/ali2gff -x "X87344" \
-y "AF100956+AF027865" \
<a href="hs-mm.sim">hs-mm.sim</a> \
> <a href="hs-mm.sim.gff">hs-mm.sim.gff</a> <BR class="hh">
</PRE></TD><TD class="codebg"> </TD></TR></TABLE></CENTER></P>
<P>
</P>
<TABLE border=0 cellpadding=0 cellspacing=0 width="100%">
<TR>
<TD class="section" width=80% ALIGN=LEFT>
<a name="RAW"></a><FONT size=5 class="K"> Raw Output </FONT>
</TD>
<TD class="section" width=20% ALIGN=RIGHT>
<a href="index.html#TOP"
onMouseover="window.status='TOP of the PAGE';">
<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
</TD></TR>
</TABLE>
<P> <BR class="hh">
</P>
<P><CENTER><TABLE class="userspace" border=0 cellpadding=0 cellspacing=0><TR><TD class="userspace" ALIGN=CENTER VALIGN=MIDDLE><CENTER><a href="hs-mm.sim.png"><IMG SRC="hs-mm.sim.s.png" ALT="Default SIM plot" HEIGHT=150 WIDTH=120 BORDER=1></a> <BR> [<a href="hs-mm.sim.png">PNG</a>] [<a href="hs-mm.sim.ps">PS</a>] [<a href="hs-mm.sim.pdf">PDF</a>] <BR>
</CENTER></TD><TD class="codebg"> </TD><TD class="codebg" ALIGN=LEFT> <BR class="hh"><PRE class="codefg">
gff2aplot.pl \
--verbose \
--percent-box-label "Identity%" \
--title "Human/Mouse MHCII Region" \
--subtitle "" \
-- <a href="hs.gff">hs.gff</a> \
<a href="mm.gff">mm.gff</a> \
<a href="hs-mm.sim.gff">hs-mm.sim.gff</a> \
> <a href="hs-mm.sim.ps">hs-mm.sim.ps</a> \
2> <a href="hs-mm.sim.log">hs-mm.sim.log</a> <BR class="hh">
</PRE></TD><TD class="codebg"> </TD></TR></TABLE></CENTER></P>
<P>
</P>
<P><CENTER><TABLE class="userspace" border=0 cellpadding=0 cellspacing=0><TR><TD class="userspace" ALIGN=CENTER VALIGN=MIDDLE><CENTER><a href="hs-mm.sim2.png"><IMG SRC="hs-mm.sim2.s.png" ALT="Command-line Customization" HEIGHT=150 WIDTH=120 BORDER=1></a> <BR> [<a href="hs-mm.sim2.png">PNG</a>] [<a href="hs-mm.sim2.ps">PS</a>] [<a href="hs-mm.sim2.pdf">PDF</a>] <BR>
</CENTER></TD><TD class="codebg"> </TD><TD class="codebg" ALIGN=LEFT> <BR class="hh"><PRE class="codefg">
gff2aplot.pl \
--verbose \
--percent-box-label "Identity%" \
--show-percent-box \
--title "Human/Mouse MHCII Region" \
--subtitle "" \
--feature-var "seqbounds::alignment_color=grey" \
--feature-var "alignment::alignment_color=red" \
--feature-var "fragment::alignment_color=green" \
--strand-var "..::strand_layer=0" \
--strand-var "++::strand_layer=2" \
-- <a href="hs.gff">hs.gff</a> \
<a href="mm.gff">mm.gff</a> \
<a href="hs-mm.sim.gff">hs-mm.sim.gff</a> \
> <a href="hs-mm.sim2.ps">hs-mm.sim2.ps</a> \
2> <a href="hs-mm.sim2.log">hs-mm.sim2.log</a> <BR class="hh">
</PRE></TD><TD class="codebg"> </TD></TR></TABLE></CENTER></P>
<P>
</P>
<TABLE border=0 cellpadding=0 cellspacing=0 width="100%">
<TR>
<TD class="section" width=80% ALIGN=LEFT>
<a name="CUST"></a><FONT size=5 class="K"> Finishing Plot for MHC Region </FONT>
</TD>
<TD class="section" width=20% ALIGN=RIGHT>
<a href="index.html#TOP"
onMouseover="window.status='TOP of the PAGE';">
<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
</TD></TR>
</TABLE>
<P> <BR class="hh">
</P>
<P><CENTER><TABLE class="userspace" border=0 cellpadding=0 cellspacing=0><TR><TD class="userspace" ALIGN=CENTER VALIGN=MIDDLE><CENTER><a href="hs-mm.sim.ini.png"><IMG SRC="hs-mm.sim.ini.s.png" ALT="Empty Plot" HEIGHT=150 WIDTH=120 BORDER=1></a> <BR> [<a href="hs-mm.sim.ini.png">PNG</a>] [<a href="hs-mm.sim.ini.ps">PS</a>] [<a href="hs-mm.sim.ini.pdf">PDF</a>] <BR>
</CENTER></TD><TD class="codebg"> </TD><TD class="codebg" ALIGN=LEFT> <BR class="hh"><PRE class="codefg">
gff2aplot.pl \
--verbose \
--percent-box-label "Identity%" \
--show-percent-box \
--title "Human/Mouse MHCII Region" \
--subtitle "" \
--x-label "Human" --y-label "Mouse" \
--custom-filename <a href="mhc2.rc">mhc2.rc</a> \
--custom-filename <a href="mhc2spc.rc">mhc2spc.rc</a> \
-- <a href="hs.gff">hs.gff</a> \
<a href="mm.gff">mm.gff</a> \
<a href="hs-mm.sim.gff">hs-mm.sim.gff</a> \
> <a href="hs-mm.sim.ini.ps">hs-mm.sim.ini.ps</a> \
2> <a href="hs-mm.sim.ini.log">hs-mm.sim.ini.log</a> <BR class="hh">
</PRE></TD><TD class="codebg"> </TD></TR></TABLE></CENTER></P>
<P>
</P>
<TABLE border=0 cellpadding=0 cellspacing=0 width="100%">
<TR>
<TD class="section" width=80% ALIGN=LEFT>
<a name="ZOOM"></a><FONT size=5 class="K"> Zooming Into the LMP2 Gene Region </FONT>
</TD>
<TD class="section" width=20% ALIGN=RIGHT>
<a href="index.html#TOP"
onMouseover="window.status='TOP of the PAGE';">
<IMG class="pnt" SRC="http://genome.imim.es/g_icons/top.gif" HEIGHT=15 WIDTH=15 BORDER=0></a>
</TD></TR>
</TABLE>
<P> <BR class="hh">
</P>
<P><CENTER><TABLE class="userspace" border=0 cellpadding=0 cellspacing=0><TR><TD class="userspace" ALIGN=CENTER VALIGN=MIDDLE><CENTER><a href="hs-mm.sim.zbox.png"><IMG SRC="hs-mm.sim.zbox.s.png" ALT="Marking area to be zoomed" HEIGHT=150 WIDTH=120 BORDER=1></a> <BR> [<a href="hs-mm.sim.zbox.png">PNG</a>] [<a href="hs-mm.sim.zbox.ps">PS</a>] [<a href="hs-mm.sim.zbox.pdf">PDF</a>] <BR>
</CENTER></TD><TD class="codebg"> </TD><TD class="codebg" ALIGN=LEFT> <BR class="hh"><PRE class="codefg">
gff2aplot.pl \
--verbose \
--percent-box-label "Identity%" \
--show-percent-box \
--title "Human/Mouse MHCII Region" \
--subtitle "Zooming into the LMP2 gene region" \
--zoom-area \
--end-x-sequence 6500 \
--end-y-sequence 6500 \
--x-label "Human X87344" \
--y-label "Mouse AF100956+AF027865" \
--custom-filename <a href="mhc2.rc">mhc2.rc</a> \
--custom-filename <a href="mhc2labels.rc">mhc2labels.rc</a> \
-- <a href="hs.gff">hs.gff</a> \
<a href="mm.gff">mm.gff</a> \
<a href="hs-mm.sim.gff">hs-mm.sim.gff</a> \
> <a href="hs-mm.sim.zbox.ps">hs-mm.sim.zbox.ps</a> \
2> <a href="hs-mm.sim.zbox.log">hs-mm.sim.zbox.log</a> <BR class="hh">
</PRE></TD><TD class="codebg"> </TD></TR></TABLE></CENTER></P>
<P>
</P>
<P><CENTER><TABLE class="userspace" border=0 cellpadding=0 cellspacing=0><TR><TD class="userspace" ALIGN=CENTER VALIGN=MIDDLE><CENTER><a href="hs-mm.sim.zoom.png"><IMG SRC="hs-mm.sim.zoom.s.png" ALT="Zooming into LMP2 region" HEIGHT=150 WIDTH=120 BORDER=1></a> <BR> [<a href="hs-mm.sim.zoom.png">PNG</a>] [<a href="hs-mm.sim.zoom.ps">PS</a>] [<a href="hs-mm.sim.zoom.pdf">PDF</a>] <BR>
</CENTER></TD><TD class="codebg"> </TD><TD class="codebg" ALIGN=LEFT> <BR class="hh"><PRE class="codefg">
gff2aplot.pl \
--verbose \
--percent-box-label "Identity%" \
--show-percent-box \
--title "Human/Mouse MHCII Region" \
--subtitle "Zooming into the LMP2 gene region" \
--zoom \
--end-x-sequence 6500 \
--end-y-sequence 6500 \
--x-label "Human" \
--y-label "Mouse" \
--custom-filename <a href="mhc2.rc">mhc2.rc</a> \
--custom-filename <a href="mhc2labels.rc">mhc2labels.rc</a> \
--custom-filename <a href="mhc2+sgp1.rc">mhc2+sgp1.rc</a> \
-- <a href="hs.gff">hs.gff</a> \
<a href="mm.gff">mm.gff</a> \
<a href="hs-mm.sgp1.gff">hs-mm.sgp1.gff</a> \
<a href="hs-mm.sim.gff">hs-mm.sim.gff</a> \
> <a href="hs-mm.sim.zoom.ps">hs-mm.sim.zoom.ps</a> \
2> <a href="hs-mm.sim.zoom.log">hs-mm.sim.zoom.log</a> <BR class="hh">
</PRE></TD><TD class="codebg"> </TD></TR></TABLE></CENTER></P>
<P>
</P>
</td>
<td class="userspace" border=0 cellpadding=0 cellspacing=0 width="10px"> </td>
</tr>
</table>
<!-- ############### TRAILER AREA ############### -->
<table class="trailer" border=0 cellpadding=0 cellspacing=0 width="100%">
<tr class="default">
<td id="traila" align=left>
<A HREF="http://genome.imim.es/main/disclaimer.html"
onMouseover="window.status='Data Release Policy and Software License';">Disclaimer</A>
</td>
<td id="trailb" align=center>
<SCRIPT type="text/javascript" languaje="javascript">
<!--
LastUpdateSplit()
// -->
</SCRIPT>
</td>
<td id="trailc" align=rigth>
<A HREF="MAILTO:gmaster@imim.es"
onMouseover="window.status='Contact with our webmaster';">webmaster</A>
</td>
</tr>
</table>
<SCRIPT type="text/javascript" languaje="javascript">
<!--
reportErrors();
// -->
</SCRIPT>
<!-- ############### EOF ############### -->
</body>
</html>
|
