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Revision: 1.12
Committed: Wed Aug 25 21:41:11 2004 UTC (11 years, 9 months ago) by skchan
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Changes since 1.11: +18 -26 lines
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added some clarifications to the doc

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8 <meta name="Description" content="Usage Manual for the Genquire© annotation package">
9 <title>Genquire&copy;</title>
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13 <dir>
14 <center><b><font size=+3>Genquire </font><font size=-2>&copy;</font></b>
15 <p><b><font size=+3>Installation and Usage Manual</font></b>
16 <p><b><font size=-1>&copy; 2001, National Research Council of Canada</font></b></center>
17 </dir>
18
19 <center><u><font size=+1>Authors:</font></u></center>
20
21 <dir>
22 <center><i>Mark Wilkinson (<font color="#0000FF"><a href="mailto:mwilkinson@gene.pbi.nrc.ca">mwilkinson@gene.pbi.nrc.ca</a></font>)</i>
23 <p><i>David Block (<font color="#0000FF"><a href="mailto:dblock@gene.pbi.nrc.ca">dblock@gene.pbi.nrc.ca</a></font>)</i><i></i>
24 <p><u><font size=+1>Installer Program:</font></u><i></i>
25 <p><i>Matthew Links (<a href="mailto:mlinks@gene.pbi.nrc.ca">mlinks@gene.pbi.nrc.ca)</a></i></center>
26 </dir>
27
28 <center><u><font size=+1>Support:</font></u></center>
29
30 <dir>
31 <center><i>Genquire GUI: Mark Wilkinson</i>
32 <p><i>Genquire Database: David Block</i>
33 <p><i>Documentation: Mark Wilkinson</i>
34 <p><i>BioPerl: <font color="#0000FF"><a href="http://www.bioperl.org">http://www.bioperl.org</a></font></i>
35 <p><i>GFF: <font color="#0000FF"><a href="http://www.sanger.ac.uk/Software/formats/GFF">http://www.sanger.ac.uk/Software/formats/GFF</a></font></i>
36 <p><i>GO: <font color="#0000FF"><a href="http://www.geneontology.org">http://www.geneontology.org</a></font></i></center>
37 </dir>
38
39 <center>GO_Perl API:&nbsp; <a href="mailto:cjm@fruitfly.bdgp.berkeley.edu">Chris
40 Mungall</a>
41 <br>&nbsp;
42 <p><u><font size=+1>Mailing Lists and CVS access:</font></u>
43 <p><u><font color="#0000FF"><a href="http://bioinfo.pbi.nrc.ca">http://bioinformatics.org/Genquire</a></font></u></center>
44
45 <p><br>
46 <br>
47 <br>
48 <br>
49 <br>
50 <br>
51 <br>
52 <br>
53 <p><b><font face="Arial"><font size=+1>INSTALLING GENQUIRE:</font></font></b>
54 <br><b><font face="Arial"><font size=+1></font></font></b>&nbsp;
55 <blockquote><b><i><font face="Arial">INSTALLATION&nbsp;IS&nbsp;BEST&nbsp;LEFT&nbsp;TO&nbsp;YOUR&nbsp;SYS-ADMIN
56 IF&nbsp;YOU&nbsp;ARE&nbsp;ON&nbsp;A&nbsp;*NIX&nbsp;SYSTEM.</font></i></b>
57 <br><b><i><font face="Arial">Root access is required to run some of the
58 installation scripts!&nbsp; This message does not affect</font></i></b>
59 <br><b><i><font face="Arial">MS Windows users...</font></i></b>
60 <br><b><i><font face="Arial"></font></i></b>&nbsp;
61 <li>
62 <font size=-1>The easiest way to install Genquire is to run the install.pl
63 program. This will install all support files<br>
64 that Genquire needs.&nbsp; In case you are interested, however, here is
65 the list of support files:</font></li>
66
67 <ul>
68 <li>
69 <font size=-1>Required Components (can be obtained from CPAN or using ActiveState
70 PPM):</font></li>
71
72 <ul>
73 <li>
74 <font size=-1>Perl 5.6 (Windows users install the latest ActiveState perl
75 release:&nbsp; <a href="http://www.activestate.com">http://www.activestate.com</a>)</font></li>
76
77 <li>
78 <font size=-1>At least BioPerl version 0.7, or bioperl-live (available by cvs from
79 <a href="http://www.bioperl.org">http://www.bioperl.org</a>)</font></li>
80
81 <li>
82 <font size=-1>Perl::Tk.</font></li>
83
84 <li>
85 <font size=-1>Perl::DBI</font></li>
86
87 <li>
88 <font size=-1>Perl::DBD-MySQL</font></li>
89
90 <li>
91 <font size=-1>Tk::JPEG</font></li>
92 </ul>
93
94 <li>
95 <font size=-1>GO Perl-API:&nbsp; contact Chris Mungall, or visit http://www.geneontology.org/#cvs&nbsp;
96 to download the API.</font></li>
97
98 <li>
99 <font size=-1>bioperl-gui can be obtained by either anonymous cvs to cvs.bioperl.org,
100 or directly from the authors (<a href="http://bioinfo.pbi.nrc.ca">http://bioinfo.pbi.nrc.ca</a>).</font></li>
101 </ul>
102 </blockquote>
103
104 <li>
105 <font size=-1><b>If you plan to run a local database</b>, you need to have MySQL
106 installed, and you must be the root user.</font></li>
107
108 <li>
109 <font size=-1>Unpack the files into your final working directory.</font></li>
110
111 <li>
112 <font size=-1><b>IF you plan to run a local database</b>, type "perl init_db.pl"
113 to initialize the database. Follow instructions given.</font></li>
114
115 <li>
116 <font size=-1>Type "perl Genquire.pl" to start the program.</font></li>
117
118 <li>
119 <font size=-1>Try connecting to the sample database, listed as "SAMPLE"
120 under the data-source menu on the startup screen. Or you can choose "GB Flat file" and choose one of the sample Genbank files to view within the ./genbank_files/ directory</font><br>
121 <br>
122 <BR></li>
123
124
125 <p><font size=-1>If you wish to install our sample data (and have write
126 access to the database you are connecting to), start the Genquire program,
127 select "Import Sequence" from the File menu on the QueryScreen window,
128 and import the sequence "sample_contig.fas". When prompted for a name,
129 give it the name "dy_c_5" (this is the name of the sequence in the FASTA
130 header). The sequence has now been imported into the database. Now select
131 "Import GFF" from the File menu and import the GFF file "sample_contig.gff".
132 All features for this sequence have now been imported to the database.
133 The sample contig may now be browsed in Genquire.</font>
134 <br>&nbsp;
135 <br>&nbsp;
136 <p><b><font face="Arial"><font size=+1>BEFORE YOU BEGIN</font></font></b>
137 <p><b><font size=-1>genquire.conf:</font></b>
138 <p><font size=-1>genquire.conf contains various path information for tools/folders
139 on your system. This file is created when you run the install script.&nbsp;
140 You may attempt to modify this file by hand using any text editor, however
141 using the install script ensures that this file is complete and in the
142 correct format.&nbsp; It should contain, at a minimum, the following information:</font>
143 <br>&nbsp;
144 <blockquote>
145 <pre><font size=-2>{
146 use lib "/path_to/bioperl-gui";
147 use lib "/path_to/bioperl-live";
148 use lib "/path_to/GO/perl-api";
149 use lib "/path_to/Genquire/PLUGINS/";
150 use lib "/path_to/Genquire";
151
152
153 $TEMP_DIR = "/tmp";
154 $BLAST_BINARIES = "/path_to/BLAST";
155 $BROWSER = "netscape";&nbsp; # command to evoke browser
156
157 $BLAST_URL = "http://URL_to/blast.cgi";
158 $WORKING_DIR = "/path_to/wherever";
159 $PLUGINS_DIR = "/path_to/Genquire/PLUGINS/";
160 $DATA_SOURCES = [["GENQUIRE_LOCAL", "gq_local.cfg"],
161 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ["GENBANK_FLAT", "gb_flat.cfg"],
162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ];
163 $BLAST_CONFIG = {
164 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # below is a list of all *acceptable* Blast parameters
165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # note that some are removed because the GUI must be able
166 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # to receive and interpret the results.&nbsp;&nbsp;
167 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # when CGI_param is not avalable for your particular CGI,
168 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # leave it undef.
169 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #
170 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # blastall_param&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #[CGI_param,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; default]
171 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '-p'&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ['blastprogram',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 'blastx'],
172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ... see the file for details...</font></pre>
173
174 <pre><font size=-2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ...};
175
176 }</font></pre>
177 </blockquote>
178 <font size=-1>Filling your local database from scripts can be difficult
179 - there are several database "flags" that Genquire uses to achieve some
180 of its features.&nbsp; If you are planning to use a local DB we highly
181 recommend that you read the Supplementary Documentation at the end of document;
182 contact the <a href="mailto:genquire-users@bioinformatics.org">mailing
183 list</a> if you have any questions.</font>
184 <br>&nbsp;
185 <p><b><font size=-1>gq_local.cfg</font></b>
186 <p><font size=-1>This file must be edited with your database login and
187 password information.</font>
188 <p><b><font size=-1>gb_flat.cfg</font></b>
189 <p><font size=-1>This file should not require any editing.</font>
190 <p><b><font size=-1>load_tigr.cfg</font></b>
191 <p><font size=-1>Change the use lib directory in the this file to point to the correct location of HelperMethods.pm. It should be ./Admin. The absolute path would be somethign like /home/skchan/gq/BIO_SUPPORT/Genquire/Admin</font>
192
193 <p><b><font size=-1>PLUGINS/plugins.conf</font></b>
194 <p><font size=-1>This file should be edited to reflect the availability
195 and location of various sequence analysis tools on your system.&nbsp; A
196 sample file is shown below:</font>
197 <blockquote><font size=-1>#Plugin_Name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
198 plugin_script,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; command-line-params</font>
199 <br><font size=-1>#______________________________________________________</font>
200 <br><font size=-1>Blast_This_Genome,&nbsp;&nbsp;&nbsp; gq_blast.pl,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
201 /tmp/,&nbsp;&nbsp; /home/markw/BLAST/</font>
202 <br><font size=-1>Remote_Blast,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
203 remoteBlast.pl,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; http://fingal/PANDA/pandablast.cgi,&nbsp;&nbsp;
204 /tmp/</font>
205 <br><font size=-1>GeneMarkHMM,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
206 GMHMM.pl,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; gmhmme, /tmp/</font>
207 <br><font size=-1>Import GFF,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
208 ImpExpGFF.pl,&nbsp;&nbsp;&nbsp;&nbsp; /tmp/</font></blockquote>
209 <font size=-1>Of the plugins included with Genquire, the necessary command
210 line arguments are:</font>
211 <blockquote><font size=-1>gq_blast: requires a temp directory, and the
212 location of the blastall executable.</font>
213 <br><font size=-1>remoteBlast.pl:&nbsp; requires the URL of the remote
214 Blast CGI and a temp directory.</font>
215 <br><font size=-1>GMHMM.pl:&nbsp; requires the command to execute the geneMarkHMM
216 executable on your system, and a temp directory.</font>
217 <br><font size=-1>ImpExpGFF.pl:&nbsp; requires a temp directory</font></blockquote>
218 <font size=-1><b>THE PLUGIN SCRIPTS&nbsp; PROVIDED WITH GENQUIRE WILL NEED
219 TO BE EDITED FOR YOUR LOCAL SYSTEM:&nbsp;</b> They contain some "use lib"
220 references which you will have to modify to reflect the location of your
221 libraries (eg. BioPerl).&nbsp; This is only a minute or two of effort.&nbsp;
222 For information on creating your own plugins, read the pod documentation
223 in <i>PlugInHandler.pm</i>, which includes a comprehensive description
224 of the relatively straightforward plugins API.</font>
225 <p><b><font size=-1>spider.pl</font></b>
226 <p><font size=-1>In order to make whole-genome annotation queries fast
227 enough to be useable, annotations are keyword-indexed by running spider.pl.&nbsp;
228 Newly entered annotations <b><i>will not</i></b> be found by quieries until
229 this script is run.&nbsp; The script erases all previous indexes and rebuilds
230 the table from scratch each time it is run.&nbsp; This process takes 10-15
231 minutes.&nbsp; You might consider running this as a cron-job each night.</font>
232 <p><b><font size=-1>Context.pm</font></b>
233 <p><font size=-1>Below is a list of the feature types that Genquire recognizes
234 by default, and the feature objects that they map onto.&nbsp; Features
235 with * are <b><i>required features </i></b>for the Genquire system to function
236 correctly!</font>
237 <br>&nbsp;
238 <blockquote>
239 <pre><font size=-1>*Gene&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =>'GQ::Server::Gene',
240 *Exon&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =>'GQ::Server::Feature',
241 *UTR&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =>'GQ::Server::Feature',
242 'TRNA Gene'&nbsp;&nbsp; =>'GQ::Server::Gene',
243 'RNA Exon'&nbsp;&nbsp;&nbsp; =>'GQ::Server::Feature',
244 Promoter&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =>'GQ::Server::Feature',
245 Intron&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =>'GQ::Server::Feature',
246 *Transcript&nbsp;&nbsp; =>'GQ::Server::Transcript',
247 *Poly_A_site&nbsp; =>'GQ::Server::Feature',
248 Misc_Feature&nbsp; =>'GQ::Server::Feature',
249 DEFAULT&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =>'GQ::Server::Feature',</font></pre>
250 </blockquote>
251 <font size=-1>&nbsp;&nbsp;&nbsp; Note that this list is <b><i>case sensitive</i></b>.&nbsp;
252 It matches a set of default features in the FeatureTypes table.&nbsp; If
253 this does not match the list of feature types you plan to work with, then
254 you will need to edit <b><i>BOTH</i></b> the names in the database and
255 the %type_hash in Context.pm (~ line 10-20 of Context.pm) by hand to add
256 new types, remove types, or change the spelling/capitalization of the equivalent
257 types... either that, or make your feature types conform to this list.&nbsp;
258 Note, however, that the starred features above <b><i>may not be changed</i></b>
259 as they will prevent Genquire from being fully functional.</font>
260 <br>&nbsp;
261 <p><b><font size=+1>Genquire Database Structure</font></b>
262 <br>&nbsp;
263 <blockquote><font size=-1>The Genquire database is designed for storing
264 information related to biological sequences.&nbsp; As such, the central
265 element of the database is the contig.&nbsp; A group of contigs that are
266 joined in a tiling path make up an assembly, and a group of assemblies
267 related in some way (i. e. release date) are a version.&nbsp; Finally,
268 there can be several versions available for each organism of interest.</font>
269 <p><font size=-1>Entering contig and supra-contig level information can
270 be done by hand, or via scripts.&nbsp; Some scripts may come with the Genquire
271 distribution, but it is recommended that this process only be attempted
272 by those with a good understanding of the Genquire schema.</font>
273 <br>&nbsp;</blockquote>
274 <b><i>Loading a Genquire Database</i></b>
275 <blockquote><font size=-1>If you are using data from TIGR, you will be
276 able to use one of the Data_* files in the ./Admin directory to load your data directly from the TIGR XML into the Genquire database.&nbsp;It would be best to run the those programs from the GUI within GenQuire, however, you can run them from the command line as well:
277 <BR>
278 <BR>
279 ie:
280 <BR>
281 your_prompt> perl Data_Dump.pl (calling the script without any arguments will show you the usage)
282 <BR>
283 <BR>
284 Genquire was designed to utilize data in TIGR XML format. However, if your data is NOT from TIGR, it's not the end of the world. A bioinformatician in your lab may be able to write parsers that can dump the data in your format into the underlying schema.</font>
285 <p><font size=-1>The Genquire database schema is available in the distribution,
286 in the file <b><i>schema</i></b>.&nbsp; An experienced Mysql administrator
287 needs no further instructions.&nbsp; If you are not so confident, run the
288 <b><i>init_db.pl
289 </i></b>script,
290 and follow the instructions.&nbsp; The
291 <b><i>init_db.pl</i></b> script
292 also enters sample organism data from the org.data file.</font></blockquote>
293
294 <blockquote>&nbsp;
295 <br><font size=-1>The first step in loading data into Genquire is to create
296 the appropriate organisms.&nbsp; The file <b><i>org.data</i></b> in the
297 Genquire distribution contains the table structure for the Organism table,
298 along with the data for two plants, Arabidopsis thaliana and rice.&nbsp;
299 Other organisms can be entered as required, either interactively, using
300 the mysql client program, or via the Genquire 'Add new organism' menu option
301 upon database login.</font>
302 <p><font size=-1>Each organism has a common name, a latin name, a short
303 code (two letter abbreviation of the latin name, in our system), and an
304 id, which is assigned automatically by the database.</font>
305 <p><font size=-1>The organism id is used in only one table, the Assembly
306 table.&nbsp; An assembly is a series of contigs in a tiling path, with
307 no gaps (i.e. Assembly is not equal to Chromosome, so if there are gaps
308 in the tiling path you may assign multiple assemblies to a single chromosome
309 to represent that).&nbsp; If one has a complete tiling path for an organism,
310 there will be one assembly for each chromosome.&nbsp; Assemblies never
311 cross chromosomes.&nbsp; Therefore, the columns of the Assembly table are
312 organism, chromosome (chr_id), version, and id (again, generated automatically
313 by the database).</font>
314 <p><font size=-1>The version column in the Assembly table refers to the
315 id of the Version table, which is a place to describe the different versions
316 of your tiling paths.&nbsp; Each version is related to its organism, so
317 organism 1 can have versions 1 and 2, and organism 2 can have unrelated
318 versions 1, 2, and 3.</font>
319 <p><font size=-1>The same contig could be placed in two different Assemblies,
320 in different versions of the tiling path.&nbsp; There is, therefore, a
321 ContigAssembly join table that relates each contig_id to its parent assembly.</font>
322 <p><font size=-1>Which brings us to contigs.&nbsp; The Contig table holds
323 only an id (auto-generated), the name of the contig (which is intended
324 to be the widely recognized designation of that contig for&nbsp; human
325 researchers), and a centromere column, which is simply y or n.</font>
326 <p><font size=-1>The sequence of the contig should be entered as a single
327 string into the database, in the Sequence table, with its contig_id.</font>
328 <p><font size=-1>The Tiling_Path table is the last table to be concerned
329 about here.&nbsp; The tiling path needs to be defined in terms of assembly
330 coordinates, and preferably in chromosomal coordinates.&nbsp; Each contig
331 then has an abs_start, which is the nucleotide coordinate, in the parent
332 assembly, of the first nucleotide of that contig sequence (seq column in
333 Sequence table), and a length, which is the length of that sequence.&nbsp;
334 Due to overlaps, you may not want to use part of your contig.&nbsp; The
335 answer to that is the virtual contig, or VC.&nbsp; The VC is defined in
336 terms of your contig, with a VC_start and a VC_length.&nbsp; So if there
337 is no overlap and the VC is the same as the contig, the VC_start equals
338 1 and the VC_length is the same as length.&nbsp; If there is some overlap,
339 the VC_length is shortened by the amount of the overlap, and the VC_start
340 may be moved, if the overlap occurs on the 5' end of the contig.</font>
341 <p><tt><font size=-1>&nbsp;assembly:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
342 ##############################################################################################################...</font></tt>
343 <br><tt><font size=-1>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
344 1&nbsp;&nbsp; 5&nbsp;&nbsp; 10&nbsp;&nbsp; 15&nbsp;&nbsp; 20&nbsp;&nbsp;
345 25&nbsp;&nbsp; 30&nbsp;&nbsp; 35&nbsp;&nbsp; 40&nbsp;&nbsp; 45&nbsp;&nbsp;
346 50&nbsp;&nbsp; 55&nbsp;&nbsp; 60&nbsp;&nbsp; 65&nbsp;&nbsp; 70&nbsp;&nbsp;
347 75&nbsp;&nbsp; 80&nbsp;&nbsp; 85&nbsp;&nbsp; 90&nbsp;&nbsp; 95&nbsp; 100&nbsp;
348 105&nbsp; 110...</font></tt>
349 <br><tt><font size=-1>&nbsp;contig:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
350 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@</font></tt>
351 <br><tt><font size=-1>&nbsp;abs_start: 24 length: 70&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
352 1&nbsp;&nbsp; 5&nbsp;&nbsp; 10&nbsp;&nbsp; 15&nbsp;&nbsp; 20&nbsp;&nbsp;
353 25&nbsp;&nbsp; 30&nbsp;&nbsp; 35&nbsp;&nbsp; 40&nbsp;&nbsp; 45&nbsp;&nbsp;
354 50&nbsp;&nbsp; 55&nbsp;&nbsp; 60&nbsp;&nbsp; 65&nbsp;&nbsp; 70</font></tt>
355 <br><tt><font size=-1>&nbsp;virtual contig:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
356 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></tt>
357 <br><tt><font size=-1>&nbsp;VC_start: 5 VC_length: 60&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
358 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
359 60</font></tt>
360 <br>&nbsp;
361 <p><font size=-1>A final note- Genquire assumes that all contigs and their
362 accompanying annotation are oriented the same way.&nbsp; If some contigs
363 in your data set are oriented in the reverse direction, you need to reverse
364 complement the contigs, and reverse the coordinates of all of its features<b><i>
365 prior to </i></b>entering them into the database.</font>
366 <p><font size=-1>FEATURES:</font>
367 <p><font size=-1>Good luck with your installation!&nbsp; Detailed questions
368 are welcome, as are improvements to this documentation.&nbsp; Please send
369 them to me, Dave, at <a href="mailto:dblock@gene.pbi.nrc.ca">dblock@gene.pbi.nrc.ca</a>,
370 and I'll reply as soon as I can.</font>
371 <br>&nbsp;</blockquote>
372
373 <p><br><b><font face="Arial"><font size=+1>STARTING THE PROGRAM</font></font></b>
374 <ul>
375 <li>
376 <font size=-1>type "perl genquire.pl" at the command line, or double-click
377 the Genquire.pl icon.</font></li>
378
379 <li>
380 <font size=-1>select a database and organism from the drop-down list</font></li>
381 </ul>
382
383 <p><br><b><i><font face="Arial">Main Genquire Window "QueryScreen"</font></i></b>
384 <ul>
385 <li>
386 <font size=-1>Select a sequence (loaded from the MySQL Contigs table),</font></li>
387
388 <li>
389 <font size=-1>Select start nt position</font></li>
390
391 <li>
392 <font size=-1>Select stop nt position (if the stop position is beyond the
393 end of the contig then the sequence/features are taken from the next contig
394 in the tiling path)</font></li>
395
396 <li>
397 <font size=-1>Select Horizontal or vertical map orientation (only vertical
398 maps allow docked annotation viewing...)</font></li>
399
400 <li>
401 <font size=-1>Then click the "Load" button (or whatever it is named on
402 your system)</font></li>
403 </ul>
404
405 <blockquote><b><i><font face="Arial">File Menu</font></i></b></blockquote>
406
407 <ul>
408 <ul>
409 <li>
410 <font size=-1>Export GFF &amp; Fasta : exports the genes/features on the
411 currently viewed contigs as GFF data, along with the associated contig
412 sequences</font></li>
413
414 <li>
415 <font size=-1>Create/Import Sequence: imports a new contig into the database
416 (would normally be followed up with importing sequence features using the&nbsp;
417 "import GFF" plugin)</font></li>
418
419 <li>
420 <font size=-1>Export annotated cDNAs : exports FASTA formatted files of
421 the cDNA and translation of the features on the annotated (blue) canvas.</font></li>
422
423 <li>
424 <font size=-1>Quit : quit</font></li>
425 </ul>
426
427 <p><br><b><i><font face="Arial">Options Menu</font></i></b>
428 <ul>
429 <li>
430 <font size=-1>switches on/off visibility of features on the visible map(s)</font></li>
431 </ul>
432
433 <p><br><b><i><font face="Arial">Tools Menu</font></i></b>
434 <ul>
435 <li>
436 <font size=-1>DockedAnnotationCanvas: prints details of annotations beside
437 the features on a vertically oriented map. Horizontal maps can not have
438 docked annotation canvases.</font></li>
439 </ul>
440
441 <p><br><b><i><font face="Arial">PlugIns Menu</font></i></b>
442 <ul>
443 <li>
444 <font face="Arial"><font size=-1>This contains all available plugins, for
445 example, running a remote Blast call, Blasting against the currently displayed
446 data, or running a gene-finder over the displayed sequence.&nbsp; <b><i>EACH
447 PLUGIN MUST BE CONFIGURED PRIOR TO USE ON YOUR SYSTEM!&nbsp;&nbsp; </i></b>See
448 the "before you begin" section above.</font></font></li>
449 </ul>
450 </ul>
451
452 <p><br><b><i><font face="Arial">Genome Map Window:</font></i></b>
453 <blockquote><font face="Arial"><font size=-1>The genome map is constructed
454 on the fly from information in the Contig, ContigAssembly, and Assembly
455 tables (see database documentation or contact <a href="mailto:dblock@gene.pbi.nrc.ca">Dave
456 Block</a> for details).&nbsp; Mouseover a contig to display it's name in
457 the QueryScreen status bar, click it to select it, double-click it to open
458 it.</font></font>
459 <p><font face="Arial"><font size=-1>Right-click on the genome map to get
460 a drop-down menu of functions:</font></font>
461 <ul>
462 <li>
463 <font face="Arial"><font size=-1>Refresh :&nbsp; re-display the last query
464 results</font></font></li>
465
466 <li>
467 <font face="Arial"><font size=-1>Query Annotations:&nbsp; brings up a query
468 dialog box in which you can enter one or more query words (select AND or
469 OR to join them) to query against the annotations.&nbsp; "hits" are flagged
470 and highlighted both on the Genome Map as well as on the Sequence Feature
471 Display Window.&nbsp; Flags are user-specific and persistent from one session
472 to the next.&nbsp; Flags take on your database username by default, and
473 are reset after every query.&nbsp; If you wish to 'archive' your query
474 results, use the "rename Current Flags' drop-down menu option to assign
475 a new flagname, which can be pulled out later using the 'View Flags of
476 type' menu option.</font></font></li>
477
478 <li>
479 <font face="Arial"><font size=-1>Remove Current Flags:&nbsp; removes all
480 currentquery-flags.</font></font></li>
481
482 <li>
483 <font face="Arial"><font size=-1>Re-name Current Flags:&nbsp; change the
484 flag-name to prevent the next query from over-writing the current query.&nbsp;
485 This 'saves' the query.</font></font></li>
486
487 <li>
488 <font face="Arial"><font size=-1>View Flags of Type:&nbsp; select a saved
489 query result and make it the current selection set.</font></font></li>
490 </ul>
491 <font face="Arial"><font size=-1><b>NOTE:&nbsp;</b> Flagging of features
492 requires that this functionality be present in the data-source adaptor
493 layer.&nbsp; Chances are, this feature will only be available when using
494 the Genquire database schema.</font></font>
495 <p><font face="Arial"><font size=-1>The Genome map also responds to clicks
496 on mapped features (in the Features table) with the primary_tag = 'dupl'.&nbsp;
497 This can be used to store duplication information as interactive features
498 in the database.</font></font></blockquote>
499 <b><i><font face="Arial">Sequence Feature Display Window:</font></i></b>
500 <ul>
501 <li>
502 <font size=-1>Single-left-click on a non-selected feature brings up the
503 details of that feature and selects it.</font></li>
504
505 <li>
506 <font size=-1>Single-left-click on a selected feature de-selects it</font></li>
507
508 <li>
509 <font size=-1>SHIFT-single-left-click on a non-selected feature adds that
510 feature to the set of selected features</font></li>
511
512 <li>
513 <font size=-1>SHIFT-single-left-click on a selected feature removes that
514 feature from the set of selected features</font></li>
515
516 <li>
517 <font size=-1>Double-left-click (sometimes triple-left-click) on a feature
518 to bring up the Hand-Annotation window to view/add/modify hand annotations</font></li>
519
520 <li>
521 <font size=-1>Left-click &amp; drag to select multiple features</font></li>
522
523 <li>
524 <font size=-1>CTRL-click &amp; drag to select an arbitrary area of sequence
525 and bring it up the Sequence Context annotation window.&nbsp; This can
526 take some time if large regions are selected!</font></li>
527
528 <li>
529 <font size=-1>CTRL-"A" (i.e. Ctrl-Shift-a) brings up a free-annotation
530 window to add a tag/value pair to all selected features. This encourages,
531 but does not force, the use of a restricted vocabulary.</font></li>
532
533 <li>
534 <font size=-1>drag-n-drop on the lower blue canvas&nbsp; to export selected
535 features as "genes".&nbsp; Features must be valid Gene feature types (i.e.
536 Exon) - there is only minor "common sense" testing done on this call, so
537 don't do anythinyting silly!</font></li>
538
539 <li>
540 <font size=-1>"C" to clear all selections</font></li>
541
542 <li>
543 <font size=-1>"P" to print (this doesn't work very well...)</font></li>
544
545 <li>
546 <font size=-1>Right-click to view pop-up menu of available commands</font></li>
547
548 <li>
549 <font size=-1>Mouseover any exon to determine if it is in-frame with the
550 currently selected exons (lights up if true)</font></li>
551
552 <li>
553 <font size=-1>Sequence Context (exons only): View selected coding-type
554 features in their sequence context in the Sequence Context annotation window
555 along with translation.</font></li>
556
557 <li>
558 <font size=-1>Sequence Context (all features) ('c' key): view all selected
559 features, including non-coding features, in their genomic context. (No
560 translation is visible)</font></li>
561
562 <li>
563 <font size=-1>Show Sequence ("s" key): View the selected features with
564 no additional genomic sequence surrounding them; selected features are
565 concatenated and translated.</font></li>
566
567 <li>
568 <font size=-1>Select sub-features is used to select the individual exons
569 which make up a gene feature on the blue canvas</font></li>
570
571 <li>
572 <font size=-1>Assign Custom Colors: allows you to re-color a feature-row
573 (one such feature must already be selected)</font></li>
574
575 <li>
576 <font size=-1>Delete From Database.&nbsp; Works on read/write features</font></li>
577 </ul>
578
579 <dir><b><i><font size=-1>Creating and Destroying Genes:</font></i></b>
580 <p><font size=-1>Once you have selected a group of features which you believe
581 belong to a gene, you can drag them to an empty portion of the Finished
582 (blue) canvas as new Gene objects. The gene will appear with a unique database-generated
583 identifier as a dark blue bar, and all of its sub-features will be visible.&nbsp;
584 Dragging features onto a gene (Blue bar), will create a new transcript
585 for that gene.&nbsp; Dragging features onto a transcript (grey bar) will
586 add the features to that transcript.&nbsp; Deleting of features is done
587 by the right-click dropdown menu.</font>
588 <p><b><i><font size=-1>Annotating Genes:</font></i></b>
589 <p><font size=-1>Gene-type objects behave exactly the same way as all other
590 on-screen objects. Double (sometimes triple) clicking them will bring up
591 the Hand Annotation window, in which you can create tag/value pairs and&nbsp;
592 GO ontology annotations for a given gene.</font></dir>
593 <b><i><font face="Arial">Chat window</font></i></b>
594 <ul>
595 <li>
596 <font size=-1>click the "update on" button to get continuous updates of
597 chat and see users who are on-line</font></li>
598
599 <li>
600 <font size=-1>click the button beside an individual user to send a message
601 to them</font></li>
602
603 <li>
604 <font size=-1>enter your message in the text-box hit enter or click "submit"</font></li>
605 </ul>
606 <b><i><font face="Arial">Hand Annotation Window</font></i></b>
607 <ul>
608 <li>
609 <font size=-1>Buttons on the right allow rapid and consistent annotation
610 of various common features. (note that it is easy to modify the AnnotationButtons.txt
611 file to create/change these buttons as you see fit)</font></li>
612
613 <li>
614 <font size=-1>Annotations are, conceptually, tag/value format. Clicking
615 a button creates a tag, and a window opens up for you to enter a value.
616 The "Enter" key completes your entry.</font></li>
617
618 <li>
619 <font size=-1>The&nbsp; "GO" button opens up a selection window below the
620 main window to allow you to middle-button-select from the available GO-ontology
621 terms.</font></li>
622
623 <li>
624 <font size=-1>deleting annotations is accomplished by shift-middle-clicking
625 over the annotation you desire to remove. N.B. - due to limitations imposed
626 by the underlying BioPerl code, **all** annotations with that particular
627 tag (i.e. all tag/value pairs with this tag) will be deleted from the annotation.
628 Annotations with other tags will not be affected.</font></li>
629
630 <li>
631 <font size=-1>All hand-annotations are live-updated into the database as
632 they are created/destroyed (i.e. not just at the end of the session - You
633 have been warned!!)</font></li>
634 </ul>
635 <b><i><font face="Arial">Sequence Context annotation window</font></i></b>
636 <ul>
637 <li>
638 <font size=-1>The selected features, their intervening sequence, +50nt
639 on either end, are displayed as colored text in the black text box. The
640 blue text box contains the associated translation of exon-type objects.</font></li>
641
642 <li>
643 <font size=-1>Features can be selected with a single left-click. The balloon-help
644 will indicate how to modify the features at the nucleotide level.</font></li>
645
646 <li>
647 <font size=-1>Features which are not already tagged as "hand-annotations"
648 are "cloned" prior to modification to prevent modification of 'hard' data
649 in the database.</font></li>
650
651 <li>
652 <font size=-1>de novo features can be created from inside the Sequence
653 Context window. Simply mouse-select the desired region, and press CTRL-SHIFT-A
654 to begin creating a new annotation. Follow the dialogue boxes to enter
655 information about this new feature.</font></li>
656
657 <li>
658 <font size=-1>Shift-C will clear any selections.</font></li>
659
660 <li>
661 <font size=-1>"a" highlights the acceptor splice sites (based on the 5
662 nt "core" consensus sequence) *see note below</font></li>
663
664 <li>
665 <font size=-1>"d" highlights the donor splice sites (based on the 5 nt
666 "core" consensus sequence) *see note below</font></li>
667
668 <li>
669 <font size=-1>"s" highlights the start codons.</font></li>
670
671 <li>
672 <font size=-1>">" and "&lt;" push out/pull in the 3? border of the selected
673 exon</font></li>
674
675 <li>
676 <font size=-1>Shift-"&lt;" -">" push out/pull in the 5? border of the selected
677 exon</font></li>
678 </ul>
679
680 <dir>
681 <dir><i><font size=-1>* this is hard-coded into the program. If you wish
682 to modify this, you need only change the regexp in the %attr{} hash at
683 the beginning of the ShowSequenceContext.pm module. The values of:</font></i>
684 <dir>
685 <dir><font face="Courier New"><font size=-1>donor_site => [regexp-value,
686 "read/write"],</font></font>
687 <p><font face="Courier New"><font size=-1>acceptor_site => [regexp-value,
688 "read/write"],</font></font></dir>
689 </dir>
690 <font size=-1>must be valid Perl regular expressions. You should also fill
691 in the values for donor_site_length and acceptor_site_length in order to
692 ensure that the sites are properly highlighted.</font></dir>
693 </dir>
694
695 <ul>&nbsp;</ul>
696 <font size=+1>Genquire Supplementary Information:</font>
697 <p><font size=-1>This information is a supplement to the installation instructions
698 for Genquire.&nbsp; It is particularly related to the data-format for certain
699 database fields which will "automagically" cause the GUI to react in useful
700 ways.</font>
701 <p><font size=-1>The <b><i>primary_tag</i></b> field of the Feature table
702 will contain many different feature types, some of which will be common
703 to most genome databases, and are thus interpreted by Genquire in a special
704 way.&nbsp; If you wish to enable this functionality, these common features
705 should have the following (case-sensitive) primary_tags:</font>
706 <br>&nbsp;
707 <br>&nbsp;
708 <table BORDER NOSAVE >
709 <tr>
710 <td><font size=-1>Table</font></td>
711
712 <td><font size=-1>primary_tag</font></td>
713
714 <td><font size=-1>type of feature described&nbsp;</font></td>
715 </tr>
716
717 <tr>
718 <td><font size=-1>Feature</font></td>
719
720 <td><font size=-1>prom</font></td>
721
722 <td><font size=-1>promotor</font></td>
723 </tr>
724
725 <tr>
726 <td><font size=-1>Feature</font></td>
727
728 <td><font size=-1>plyA</font></td>
729
730 <td><font size=-1>polyadelylation site</font></td>
731 </tr>
732
733 <tr>
734 <td><font size=-1>Feature</font></td>
735
736 <td><font size=-1>dupl</font></td>
737
738 <td><font size=-1>duplicated region*</font></td>
739 </tr>
740 </table>
741
742 <p><font size=-1>Annot_Feature, Annot_Gene, and&nbsp; Annot_discard should,
743 preferably, not be filled in by hand as the entries for these tables come
744 from within Genquire itself.</font>
745 <p><font size=-1>*w.r.t. the annotation of duplicated regions:&nbsp; additional
746 information about duplications is held in the TagValue, Tags and Values
747 tables as follows:</font>
748 <br>&nbsp;
749 <br>&nbsp;
750 <table BORDER NOSAVE >
751 <tr>
752 <td><font size=-1>Table</font></td>
753
754 <td><font size=-1>tag</font></td>
755
756 <td><font size=-1>value</font></td>
757 </tr>
758
759 <tr>
760 <td><font size=-1>TagValue</font></td>
761
762 <td><font size=-1>Homology_to</font></td>
763
764 <td><font size=-1>Contig.name (from the Contigs table)</font></td>
765 </tr>
766
767 <tr>
768 <td><font size=-1>TagValue</font></td>
769
770 <td><font size=-1>Homology_start</font></td>
771
772 <td><font size=-1>start position on the homologous contig</font></td>
773 </tr>
774
775 <tr>
776 <td><font size=-1>TagValue</font></td>
777
778 <td><font size=-1>Homology_stop</font></td>
779
780 <td><font size=-1>end position on the homologous contig</font></td>
781 </tr>
782
783 <tr>
784 <td><font size=-1>TagValue</font></td>
785
786 <td><font size=-1>Orientation</font></td>
787
788 <td><font size=-1>direct or inverted (this is only relevant for dups on
789 the same chromosome)</font></td>
790 </tr>
791 </table>
792
793 <p><font size=-1>In addition to the tags above, there are certain Feature.primary_tag's
794 that will be <b><i>completely ignored</i></b> by Genquire - i.e. features
795 with these primary_tags <b><i>will</i></b> <b><i>not</i></b> be mapped,
796 and <b><i>will not</i></b> be visible on the annotation canvas&nbsp; This
797 was done to allow display of BioPerl-parsed genbank entires.&nbsp; The
798 ignored primary_tags are (case sensitive):</font>
799 <br>&nbsp;
800 <ul>
801 <li>
802 <font size=-1>source</font></li>
803
804 <li>
805 <font size=-1>CDS_span</font></li>
806
807 <li>
808 <font size=-1>intron</font></li>
809
810 <li>
811 <font size=-1>gene_span</font></li>
812
813 <li>
814 <font size=-1>CDS</font></li>
815 </ul>
816
817 <p><br><font size=-1>The BlastLookUp table holds the ids (primary keys)
818 of the BlastAcc table for exon_id's which share an NCBI&nbsp; gi accession
819 number in common from their Blast homology.&nbsp; This table is difficult
820 to generate by hand/script, and is best done within Genquire if possible
821 using the Blast Exon(s) function on the pop-up menu.&nbsp; When full, this
822 table allows the selection of all exons on a canvas which share common
823 Blast hits (useful for finding gene boundaries).</font>
824 <p><font size=-1>The Blast_vs_EST table is fairly self-explanatory - EST's
825 are (outside of Genquire) Blasted against the genome of the organism, and
826 the Blast reports are parsed into this table.&nbsp; When parsing Blast
827 data into the EST and Blast_versus_EST tables, the "query" is considered
828 to be the EST, adn the "subject" is considered to be the contig/genome.&nbsp;
829 EST's (or other transcript-based sequences like cDNA's) may then be mapped
830 onto your annotation canvas, and used in Sim4 alignments.&nbsp; Information
831 about the EST itself is held in the EST table.&nbsp; Note that both the
832 EST table and the Blast_versus_EST tables have a "source" column, and this
833 needs to be consistent between the two tables.</font>
834 <br>&nbsp;
835 <br>&nbsp;
836 </body>
837 </html>