Analyzing Human GENOME by Genome Explorer

webmaster webmaster at softberry.com
Wed Apr 4 03:32:52 EST 2001


Analyzing Human GENOME by Genome Explorer
=========================================================
--------- 1st version of Softberry Genome Explorer

          http://www.softberry.com/genomb/chrvis.html 

Softberry Genome Explorer allows visualization of many genome features, such 
as known and predicted genes, mRNAs, EST, known genes and many others, on 
large genomic sequences. On this server, Genome Explorer shows these 
features for human genome draft from UCSC Human Genome Project Team. In 
addition to publicly available information, Genome Explorer includes genes 
predicted by Softberry's FGENESH++ program. Genome Explorer can be used to 
extract nucleotide and protein sequences of particular genes, functional sites and 
other features. Most of sequence-extracting functions are disabled here due to 
computer resource constraints, except for protein sequences of genes predicted 
by FGENESH++. These sequences can be viewed by right-clicking genes of 
interest in Gene Explorer's main window. 

Gene Explorer use starts with 

Selecting Chromosome Region. 

Chromosome can be selected from Chromosome Selection Dialog Box. To open 
it, either choose Options> Chromosome from main menu or press Chromosome 
button. In Chromosome Selection Dialog Box, select chromosome from pull-
down list. Then select chromosome region to be loaded. It can be done using a 
ruler just below pull-down list, or by entering selected sequence boundaries' 
positions in fields FROM, TO and/or SIZE. By default, a 600-kb fragment of 
chromosome 1 is loaded. Please keep in mind that the larger selected region, the 
longer it will take to load and the slower to navigate. 

Ruler is a graphical representation of given chromosome. You can chose region 
to load by moving and reshaping selection (green shaded rectangle) along its 
length:
- Dragging selected region by mouse to the left or to the right;  
- Dragging one of the region's boundaries;  
- Shift-dragging region's boundary - in this case both boundaries 
expand or retract to the same extent. 
 
Boundaries of selected region are displayed in fields FROM and TO below 
chromosome's map, and its size in SIZE field. To select by sequence position, 
enter start and end positions in the fields FROM and TO, or start (end) position 
and length in fields FROM (TO) and SIZE. Press ENTER key or move cursor to 
another field to record entered values. If entered values in any of the fields go 
beyond chromosome's boundaries, they are corrected and new values are 
displayed in the fields. Changing value in one of the field may result in change in 
another - e.g. entering new value in FROM will change value in SIZE. Selected 
region may be shifted to the left or to the right by pressing buttons <<LEFT and 
RIGHT>>. The size of the shift must be entered in the field between these two 
buttons. Default value is 10 MB. After selection is made, pressing OK closes 

Chromosome Selection Dialog Box and displays part of selected region in 

Explorer's main window. 

Selecting Features to Display. 

Selecting Features to display can be done by either pressing FEATURES button 
or choosing Options> Features from main menu. Small window with a list of 
features opens. You can select any combination or all of them. The list includes: 

Gap locations (on nucleotide sequence)  
Golden Path Positions of chromosome segments  
Gold chromosome assembly  
Genes predicted by FGENESH++ program  
Known genes (from GenBank/Infogen entries)  
Known mRNA sequences  
Known EST sequences  
Repeat locations  
Chromosome cytogenetic band locations. 

By default all features are selected. 

Navigating Main Window

After choosing chromosome region and features, a fragment of loaded region is 
displayed in the main window. You can change size and location of displayed 
fragment using ruler and boundary/size fields the same way you did it in 
Chromosome Selection Dialog Box. But in the main window, a ruler represents 
loaded chromosome region rather than whole chromosome. 
You can also move along the region's length by dragging main window map by 
mouse to the left or to the right. Shift-drag to the left decreases map resolution, 
while same move to the right increases it. If option "Repaint on Drag" is enabled 
(default), the map will move along with mouse. If it is disabled, map is redrawn 
only after mouse button is released. If you have slow Internet connection, disable 
this option. Finally, you can chose a region on the map by Ctrl-dragging, and this 
region will expand over whole window. Maximal resolution of Genome Explorer is 
one base pair per pixel.

Features of selected region are displayed in the middle section of main window. 
Each feature type is shown on its own line(s). If features of same type overlap on 
sequence, they are shown on separate lines. 
When mouse pointer touches some feature on the map, it changes its shape to a 
hand. At that time, if option "Show Information on Mouse Over" is enabled 
(default), available information on each feature is shown in left bottom panel 
(Feature Info Panel). If that option is disabled, you must click left button to get 
information displayed. If mouse pointer is located over multi-block feature, like 
several-exon gene or EST with several alignment blocks, Feature Info Panel is 
divided into two sections. In left section, information about whole section is 
displayed, while in right section, information about selected (pointed to) block.
Mouse right-clicking on gene predicted by FGENESH++ opens a separate 
window that displays that gene's amino acid sequence.
On top of main window's ruler, there are buttons "Back" and "Forward" which 
operate in a way similar to same buttons in Internet browsers.

Menu Descriptions. 

File menu:

Exit - exit the viewer.

Options menu:

Chromosome - Chose chromosome to view. 

Features - Chose features to view. 

Repaint on Drag - If enabled (default), view is updated continuously when drag operation 
is performed by mouse. If disabled, view is updated only when drag operation is finished 
(mouse button released). 
Show Information on Mouse Over - If enabled (default), information on functional site is 
displayed if mouse is located over that site. If disabled, information is displayed after a 
click on a functional site. 
Show Navigation Line (default enabled) - displays vertical line at the location of mouse 
pointer. 
Allow Visual Map Navigation (default enabled) - allows dragging of displayed region by 
mouse.

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