Table of Contents

Introduction
Menu
Mouse Actions and Hotkeys

Introduction

MyGV is an application to visualize (potentially genome-scale) gene structure annotation and prediction. The program was designed in particular to display output of our spliced alignment algorithm GeneSeqer, however output of other programs such as GENSCAN or GeneMark.hmm can also be displayed after transformation to a generalized MyGV input format. Gene structure predictions can be compared with existing gene structure annotation in GenBank format.

This program is written in JAVA and should work on any platform supporting JAVA.

Please direct all communications related to this software to:

Volker Brendel
Department of Zoology & Genetics
Iowa State University
Ames, IA 50011-3260
U.S.A.

Phone:      (515) 294-9884; Fax: (515) 294-6755
email:        vbrendel@iastate.edu

 

The following is a snapshot of MyGV, produced by the command "java MyGV -d ATFCA5 -g gsq.ATFCA5 -i gsn.ATFCA5.giif glm.ATFCA5.giif gm.ATFCA5.giif" in the MyGV1.0 demo/PMB/FIG1and4 directory:

The display is divided into five regions (Note: The relative sizes of the different panels are adjustable and may have to be changed in particular applications to display all data):

1, Toolbar.  There are 10 icons on the left side of the toolbar, the leftmost three of which are linked to the menu items in the "File" menu, the rightmost two are linked with items in the "Help" menu, and the middle ones link functions controlling region 4 (ASV).    The next two text fields "Start" and "End" are to specify the region to be displayed (actived by pressing "Go" button). This selection is particularly useful when the user wants to analyze only some small region of a very long genomic sequence (eg., an entire chromosome).  (Note: Given enough memory, MyGV could load the GeneSeqer output for a complete chromosome.   However, because many GUI components are invoked, display speed will become very slow.)   The "Zoom" field is to show and select the current zoom level (between 1 and 250).

Open16.gif (228 bytes)   Open Files Add16.gif (238 bytes)   Add Files Print16.gif (293 bytes)  Print out ASV Back16.gif (183 bytes)   Left shift
Forward16.gif (183 bytes)  Right shift ZoomOut16.gif (304 bytes)  Zoom out ZoomIn16.gif (304 bytes)  Zoom in Information16.gif (661 bytes)  Mark all labels
Help16.gif (661 bytes)   Show this file About16.gif (644 bytes)  Show ABOUT

2, Annotation List Tree (ALT) panel.  The checked boxes correspond to the GenBank GI identifiers of aligned ESTs.  A "+" following theGI identifier indicates alignment of the strand corresponding to the GenBank entry, whereas a "-" indicates alignment of the complementary strand.  AGS, Alternative Gene Structures, represent the consensus of

3, Annotation Overview (AO) panel. Annotated and predicted genes are represented by arrows from 5'- to 3'-extent of the coding region.  Color scheme: GenBank (GB), blue;  AGS, green;  EST, red;  GENSCAN(GSN), cyan;  GlimmerM (GLM), pink;  GeneMark.hmm (GM), gray. The vertical green lines delineate the region of the input sequence analyzed in detail in the Annotation Scalable View (ASV) panel. Pressing the tab "Text Information" will display the original text output linked to the selected annotation.

4, Annotation Scalable View (ASV) panel. The colorscheme in the ASV panel is the same as in the AO panel, except that exon quality scores assigned by GeneSeqer and GENSCAN are color-coded. For both programs, the quality scores are normalized to a maximal value of 1.0.   Exon are represented by colored boxes as follows: red,score > 0.9; pink, score > 0.8; cyan, score > 0.7; light gray, score > 0.6; gray, otherwise.  Introns are shown as horizontal lines connecting the exon boxes.  Splice site scores given by GeneSeqer and GENSCAN are indicated by vertical lines of proportional lengths flanking the introns.

5, Text Data Overview (TDO) panel. This panel tabulates details of the (predicted) exon or intron marked by the blue cross in the ASV panel.  Pd, donor site score.   Sd, similarity score for donor site flanking50 nucleotide exon region.   Pa, acceptor site score.  Sa, similarity score for acceptor site flanking 50 nucleotide exon region.

 

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Menu

File Open  Open annotation/gene prediction output files; supported formats: GenBank, FASTA, GeneSeqer output, output of other gene prediction programs in GIIF
Append Similar as "Open", but append the new files without closing those already opened
Close Close and exit MyGV
Save Partial View Save the ASV panel as a JPEG image
Print Print the ASV panel
Gene Prediction Run_GENSCAN Run local GENSCAN via ./scripts/Run_GENSCAN
Run_GeneMark.hmm Run remote GeneMark.hmm web service via ./scripts/Run_GeneMark.hmm
Help Introduction Show this HTML file
About Display ABOUT dialog
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Mouse Actions and Hotkeys

AO Panel Click (when cursor is hand-like) Scroll the green rectangle and the corresponding ASV panel
Click (when cursor is arrow) Display attributes of the selected item in the TDO panel
Drag and Drop Select a region for gene prediction 
ASV Panel Left-Click on the annotation label Show information about the selected annotation in the AO (toggle the "Text Information" tab on) and TDO panels. The selected element (exon or intron) is marked by a blue cross.
Left-Click on the panel Scroll the ASV panel and the green rectangle in the AO panel accordingly
Right-Click on the annotation label Pop up a menu for Mark/Unmark-ing or Deleting the label and Reversing the display arrow
Right-Click on the panel Pop up a menu for (1) Saving the Partial View currently displayed in the panel, (2) Saving the Complete View (all data in the range), (3) Mark/Unmark-ing all labels, (4) Clearing the blue cross, and (5) Refreshing the display.
Ctrl + Left-Click on the annotation label Hide the label
Shift + Left-Click on the annotation label Mark/Unmark the label ("Refresh" afterwards)
Left-DoubleClick on the annotation label Show the putative transcript and indicate long open read frames (>64bp; blue underline)
ALT panel Left-Click Select label and center the AO and ASV panels on the label
Left-DoubleClick Hide or Unhide the label
Ctrl + Left-Click Hide or Unhide the label, same as Left-DoubleClick

 

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Wei Zhu and Volker Brendel.
Copyright © [Iowa State University]. All rights reserved.
Revised:  December 4, 2001.