GeneStudio, Inc. Molecular Biology Software

(Latest version: 2.1.1.5 released December 13, 2007)
GeneStudio™ Pro is a modern suite of molecular biology applications for the Windows platform built on our sequence format conversion engine, SeqVerter™. All manipulations with sequences of different formats are thus seamless and transparent for the user. In addition, GeneStudio™ Pro is very well integrated with the information available for molecular biologists on the Internet (please make sure to read the NCBI Disclaimer and copyright information before using Entrez and BLAST).

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.
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. In comparison to available command-line programs, Web-based utilities or programs accessed from a UNIX machine through an X-Windows interface, GeneStudio™ Pro can be mastered in a very short time.

Main changes in version 2.x

The Alignment and Contig editors will now accommodate sequences longer than 500,000 bases and process them much faster than the previous versions.
Following suggestions from users, we 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).
Quality score of traces from Applied Biosystems DNA sequencers may be displayed as a visual aid to their quality,
Following the release of the new PHYLIP 3.6 package of programs for inferring phylogenies we offer the user the option to choose version 3.5 or 3.6.
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.
All dialogs are now compatible with the East Asian versions of Windows.
GeneStudio Pro was compiled to be Unicode compatible.
GeneStudio Pro has a new look and feel of the visual components.

System and Hardware Requirements:

Windows 2000, XP, Vista
Pentium 450-megahertz (MHz) or faster processor
180 MB hard disk space available
512 MB RAM
Internet connection required to search online databases (Entrez and BLAST)

Current GeneStudio™ Pro components

GeneStudio™ Pro is a modern, modular suite of programs for molecular biologists. GeneStudio™ Pro is currently available with three components: SeqVerter, Alignment editor, and Contig editor. Other components, such as Primer design will be added in the near future.

SeqVerter

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 special viewers:

Sequence viewer displays the raw sequence information of a given file, including automatic DNA chromatograms.
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.
Trace viewer is a very convenient utility for viewing, scaling, and printing of automatic DNA sequencer traces (chromatograms).
Pretty view allows to format and color the sequence in many different ways and to export the view to a word-processor file (*.rtf) or to Copy/Paste the formatted sequence into word processor or presentation documents.

Alignment editor

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 method, such as fastDNAml (including 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.

Contig editor

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.

Flexible workspace
	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.

GeneStudio™ Pro is a modern application developed for the 21st century. It is very different from older programs that were recompiled from Mac® (Macintosh computers, Apple Computer, Inc.) applications and often poorly adapted to the requirement of the Microsoft Windows user interface or were developed for pre-PCR times, when cloning, restriction enzyme mapping, and vector manipulation were techniques of the day.

Please download GeneStudio Pro and see how fast it can be mastered without intensive and expensive training or even without viewing the GeneStudio tutorials. If you like GeneStudio Pro, you will be surprised to find out that it is priced very competitively. Moreover, we offer substantial discounts for users: (i) from countries outside North America (Canada & United States), the European Union, Norway, Switzerland, Australia, New Zealand, Hong Kong, Japan, Singapore, South Korea, and Taiwan; (ii) from Government, Non-profit, and Educational institutions; (iii) who can prove ownership of competing software. Multiple discounts may be combined.