GeneStudio™ Pro
Category Cross-Omics>Sequence Analysis/Tools
Abstract GeneStudio Pro is an advanced suite of molecular biology applications for the Windows platform built on the manufacturers sequence format conversion engine, SeqVerter.
All manipulations with sequences of different formats are thus seamless and transparent to the user.
In addition, GeneStudio Pro is very well integrated with the information available for molecular biologists on the Internet.
- a) A convenient interface to Entrez allows the user to search GenBank and retrieve sequences of choice directly into a sequence alignment or a contig assembly project.
- b) Basic Local Alignment Search Tool (BLAST) searches can be done through a simple right click on a sequence or on a selected fragment of a sequence. BLAST results are retrieved and stored on the user’s computer and can be viewed at any time.
GeneStudio Pro has an intuitive, user-friendly interface; most operations are done through drag-and-drop operations or through simple, uncluttered menus.
GeneStudio Pro is currently available with three (3) components: SeqVerter, Alignment editor, and Contig editor.
1) SeqVerter -- (also known as GeneStudio LE) is a free application that will continue to function in an unregistered version of GeneStudio Pro.
It contains all the popular sequence format conversion and manipulation functions of the stand-alone, dialog-based SeqVerter. The SeqVerter component of GeneStudio Pro adds Internet integration (Entrez and BLAST), efficient file management, and four (4) special viewers:
- a) Sequence viewer displays the raw sequence information of a given file, including automatic DNA chromatograms.
- b) File view displays the complete information contained in a sequence file. In a GenBank file, links to PubMed and other information will be detected and are accessible inside the viewer.
- c) The Trace viewer is a very convenient utility for viewing, scaling, and printing of automatic DNA sequencer traces (chromatograms).
- d) The Pretty view allows you to format and color the sequence in many different ways and to export the view to a word-processor file rich text format (*.rtf) or to Copy/Paste the formatted sequence into the word processor or presentation documents.
2) Alignment editor -- is a very convenient interface to sequence alignments methods (currently, only to the fully-licensed CLUSTAL W program v. 1.83).
It has several word processor-like functions (including Undo and Redo) facilitating tasks required to prepare alignments for publication, selection of conserved regions for primer design and for molecular phylogeny.
This component has a built-in interface to several popular phylogeny reconstruction methods, such as fastDNAml (including the Windows implementations of the fastDNAml_boot and fastDNAml_loop scripts);
DNADIST/NEIGHBOR, DNAML, and DNAPARS programs from the PHYLIP package (including automatic implementation of SEQBOOT and CONSENSE); as well as TREE-PUZZLE.
Results from the analyses can be sent for viewing of the phylogenetic trees to the popular TreeView program directly from the Alignment editor.
3) Contig editor -- is a sophisticated program for sequence assembly and editing from automatic DNA sequencer traces.
Modern design allows smooth adjustments of horizontal and vertical scaling of the trace display while other windows of the GeneStudio’s workspace may be closed to maximize the view of the traces.
Moreover, contigs or their fragments can be conveniently selected for BLAST searches that are processed in the background. The user may open a ruler with translation of the contig in all or any of the 6 reading frames.
The GeneStudio workspace is very flexible. All of the screen elements except for the main window can be hidden with a click of the mouse to maximize the display area for editing contigs or alignments.
Main changes in version 2.x of GeneStudio Pro --
1) The Alignment and Contig editors will now accommodate sequences longer than 500,000 bases and process them much faster than the previous versions.
2) Following suggestions from users, the manufacturer included translation of sequences loaded into the Alignment editor as an aid in aligning sequences manually. Such mixed DNA/protein alignments may be saved in the new GSA format (*.gsa - GeneStudio Alignment).
3) Quality score of traces from Applied Biosystems DNA sequencers may be displayed as a visual aid to their quality.
4) Following the release of the new PHYLIP 3.6 package of programs for inferring phylogenies the manufacturer offers the user the option to choose version 3.5 or 3.6.
5) Handling of the output of phylogeny programs was modified to give the user a choice to use the soon to be release GSTree (GeneStudio Tree) program instead of the TreeView tree display program.
6) All dialogs are now compatible with the East Asian versions of Windows.
7) GeneStudio Pro was compiled to be Unicode compatible.
8) GeneStudio Pro has a new look and feel of its visual components.
System Requirements
Currently, the manufacturer's programs target the Windows platform only.
- Windows 2000, XP, Vista
- Pentium 450-megahertz (MHz) or faster processor
- 180 MB hard disk space available
- 256 MB RAM
- Internet connection required to search online databases (Entrez, BLAST).
Manufacturer
- GeneStudio, Inc.
- P.O. Box 857
- Suwanee, GA 30024-0857 USA
- Tel. (866) 954-3889 (toll free from North America)
- International: +1 (250) 954-3889
- Fax: +1 (770) 822-0123
- E-mail (preferred for fast response): info@genestudio.com
Manufacturer Web Site GeneStudio Pro
Price Contact manufacturer.
G6G Abstract Number 20076R
G6G Manufacturer Number 101115