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New options to analyze Human GENOME by Genome Explorer

webmaster webmaster at softberry.com
Wed May 16 04:45:53 EST 2001

New options to analyze Human GENOME by Genome Explorer  
--------- 2nd version of Softberry Genome Explorer  INCLUDES Search possibility to 
find location of EST/mRNA in genome if you know its AC GenBank and tools for 
Extracting and visualization sequences of genes and their coding regions  
Softberry Genome Explorer allows visualization and sequence extraction 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. These sequences can be viewed by right-clicking features of 
interest in Gene Explorer's main window. 

Searching Genome for Feature of Interest

Genome Explorer has search function that help you visualize feature of interest 
on a genome. Features can be searched by GenBank AC number (mRNAs and 
known genes), EST ID, cytogenetic band name, repeat name or FGENESH++ 
predicted gene ID. Search can be performed only on feature types loaded into 
memory (Options > Load Feature Types option, see below). To start search, 
press FIND FEATURE button or select Search > Find Feature option from a 
menu. Find Feature dialog is displayed, where you can specify search conditions. 
After search was performed, a list of found features is displayed. To view a 
feature and its surroundings on genome map, click on a feature from the list and 
press LOAD button. List of found features is stored in memory until new search is 
performed or Genome Explorer is exited.

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 the 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. 
The ruler is a graphical representation of entire given chromosome. You can 
choose 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. 

Options > Load Feature Types menu option allows you select features to be 
loaded in computer memory. Of these loaded, some or all can be displayed in 
Genome Explorer window. Selecting Features to display can be done by either 
pressing FEATURES button or choosing Options> Features from main menu. 
The following features can be selected: 
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 
SNPs from clone overlaps 
SNPs from random reads 
Sequence Tag Marker locations 
Repeat locations 
Mouse syntheny regions 
Chromosome cytogenetic band locations. 

By default all features are selected in both LOAD FEATURES TYPES and 
FEATURES dialogs. Search can be performed only among loaded features.
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 moves along with mouse. If it is disabled, map is redrawn only 
after mouse button is released. Finally, you can choose 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). By default, if features of same type 
overlap on sequence, they are shown on separate lines, while top line for each 
type of features (shaded in gray) shows all features of that type combined. You 
can switch off display of combined lines or separate lines by chosing Options > 
Feature Show Mode > All Objects or > Combined Objects.
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 (multi-exon) 
feature, like gene or EST with several alighnment 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.
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.

Mouse right-clicking anywhere on the map opens a menu with the following 

Show Sequence - (+) and (-) - Shows nucleotide sequence around 
the point clicked, positive or negative strand.  
Show Feature Sequence - (+) and (-) - Shows nucleotide sequence 
of a given feature on either of two strands, as well as short flanks. 
Enabled only when pointer is located over a feature (hand-shaped).  
Show Block Sequence - (+) or (-) - shows nucleotide sequence of a 
given block (exon).  
Show Protein - Shows amino acid sequence of gene product. 
Enabled only if gene is pointer is located over a gene. 
Show Entry - Shows GenBank entry for mRNA or EST.
Sequences and entries are shown in a separate window. Options of sequence 
display are determined by Sequence Options menu (Options>Sequence). 
Sequences of selected features are shown in bold capital letters, while flanks are 
shown in lowercase. Exons on exon-containing features (gene, mRNA, EST), are 
highlighted in blue. Selected exons, if any, are shown in red.
Menu Descriptions. 

File menu:

Exit - exit the viewer.

Search menu:

Find Feature - opens dialog for feature search. 

Found Feature List - shows last feature search results. 

Options menu:

Chromosome - Choose chromosome to view. 

Features - Choose features to view (only those loaded by Load 

Feature Type can be viewed). 

Load Feature Types - choose features to load in computer memory. 

Sequence - Select sequence display options: flank lengths for 
feature sequence display, length of sequence to be displayed, 
numbering options etc. 

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 

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 navigation 
by dragging map by mouse to the left or to the right. 

Feature Show Mode - choose between displaying overlapping 
features of same type on separate lines (All Objects), on one line 
(Combined Objects) or both. Also, Full Mode displays each 
individual known overlapping EST or mRNA on a separate line, 
while Compact Mode displays only one EST/mRNA of a class.


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