Menu
▾
▴
[Gmod-apollo-cmts] CVS: apollo/doc/html userguide.html,1.10,1.11
|
From: Nomi H. <no...@us...> - 2002-10-30 00:17:45
|
Update of /cvsroot/gmod/apollo/doc/html In directory usw-pr-cvs1:/tmp/cvs-serv23247 Modified Files: userguide.html Log Message: Index: userguide.html =================================================================== RCS file: /cvsroot/gmod/apollo/doc/html/userguide.html,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** userguide.html 23 Oct 2002 00:24:20 -0000 1.10 --- userguide.html 30 Oct 2002 00:17:42 -0000 1.11 *************** *** 118,122 **** <a href="#Edit">Using Apollo to edit annotations</a> <UL> ! <a href="#Saving">Saving data</a><BR> </UL> <a href="#Configuration">Configuring Apollo</a><BR> --- 118,129 ---- <a href="#Edit">Using Apollo to edit annotations</a> <UL> ! <LI><a href="#Saving">Saving your annotations</a><BR> ! <LI><a href="#Autosaving">Autosaving</a><BR> ! <LI><a href="#TranscriptColoring">Transcript coloring</a><BR> ! <LI><a href="#CreatingGene">Creating a gene model </a><BR> ! <LI><a href="#ModifyingGene">Modifying gene models</a><BR> ! <LI><a href="#AnnotationText">Editing annotation text</a><BR> ! <LI><a href="#ExonDetailEditor">Exon detail editor</a><BR> ! <LI><a href="#"></a><BR> </UL> <a href="#Configuration">Configuring Apollo</a><BR> *************** *** 970,974 **** <H1><a name="Edit"></a>Using Apollo to edit annotations</H1> ! [NOTE: THIS SECTION NEEDS A LOT OF WORK. Some subsections are just notes from the curators, which may be out of date. Also, need more screenshots.] <P> --- 977,981 ---- <H1><a name="Edit"></a>Using Apollo to edit annotations</H1> ! [NOTE: THIS SECTION NEEDS WORK. Some subsections are just notes from the curators, which may be out of date. Also, need more screenshots.] <P> *************** *** 991,995 **** results, but is not the best choice for saving annotations. ! <H3>Autosaving</H3> In order to protect against losing changes that you've made to the annotations, Apollo automatically saves your data every 30 minutes (that interval can be --- 998,1002 ---- results, but is not the best choice for saving annotations. ! <H3><a NAME="Autosaving"></a>Autosaving</H3> In order to protect against losing changes that you've made to the annotations, Apollo automatically saves your data every 30 minutes (that interval can be *************** *** 1019,1023 **** same result. ! <H4>Transcript coloring</H4> If AutoTranscriptColoring is set to "true" in apollo.cfg, transcripts are colored according to their creator. By default, AutoTranscriptColoring is off and --- 1026,1030 ---- same result. ! <H4><a NAME="TranscriptColoring"></a>Transcript coloring</H4> If AutoTranscriptColoring is set to "true" in apollo.cfg, transcripts are colored according to their creator. By default, AutoTranscriptColoring is off and *************** *** 1029,1034 **** </pre> ! <h3>Creating a gene model</h3> ! To create a gene model, you can simply select results on which to base the gene annotation and drag them into the blue annotation zone. For example, in this screenshot, the user has chosen a purple Genie prediction from the reverse strand and dragged it into the annotation area. --- 1036,1041 ---- </pre> ! <h3><a NAME="CreatingGene"></a>Creating a gene model</h3> ! To create a new gene model or transcript, you can simply select results on which to base the gene annotation and drag them into the blue annotation zone. For example, in this screenshot, the user has chosen a purple Genie prediction from the reverse strand and dragged it into the annotation area. *************** *** 1036,1047 **** <P><center><img SRC="images/drag-to-create-gene-model.gif" width=146 height=196></center><P> As you drag the selected result(s), you will see a ghost image. When you drop them, ! a gene model will be created. If there is already a gene transcript overlapping the ! region covered by the result, the new annotation will be a new transcript of that gene. <P> Another way to create a gene model is by selecting features and using the right mouse ! popup menu option "Create gene model". A new annotation of that structure will appear in the evidence zone. ! (If you select exons from more than one gene a merge will occur.) ! <h3>Modifying gene models</h3> <H4>Deleting exons</H4> --- 1043,1060 ---- <P><center><img SRC="images/drag-to-create-gene-model.gif" width=146 height=196></center><P> As you drag the selected result(s), you will see a ghost image. When you drop them, ! a gene model will be created. If there is already a gene transcript whose ORF overlaps the ! ORF covered by the new stranscript, you will be asked whether the new transcript should be added ! to the overlapping gene or made into a new gene. <P> Another way to create a gene model is by selecting features and using the right mouse ! popup menu option "Create gene transcript". A new annotation of that structure will appear in the evidence zone. ! (If you select exons from more than one gene you will be asked whether you ! want the genes to be merged.) ! <P> ! If you know you want to create a new overlapping gene, rather than a transcript ! belonging to an existing gene, you can bypass the dialog by using the "Create new ! overlapping gene" menu item. ! <h3><a NAME="ModifyingGene"></a>Modifying gene models</h3> <H4>Deleting exons</H4> *************** *** 1150,1154 **** <P> ! <H3>Editing annotation text</H3> To bring up the annotation text editor for a transcript, choose the "Annotation info" option --- 1163,1167 ---- <P> ! <H3><a NAME="AnnotationText"></a>Editing annotation text</H3> To bring up the annotation text editor for a transcript, choose the "Annotation info" option *************** *** 1197,1201 **** <P> ! <h3>Exon detail editor</h3> The exon detail editor can be invoked from the right-mouse popup menu. --- 1210,1214 ---- <P> ! <h3><a NAME="ExonDetailEditor"></a>Exon detail editor</h3> The exon detail editor can be invoked from the right-mouse popup menu. *************** *** 1877,1881 **** <HR><P> <!-- hhmts start --> ! Last modified: Tue Oct 22 17:19:52 PDT 2002 <!-- hhmts end --> --- 1890,1894 ---- <HR><P> <!-- hhmts start --> ! Last modified: Tue Oct 29 16:16:33 PST 2002 <!-- hhmts end --> |