GeneStudio Pro

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.

System and Hardware Requirements:

  • 32-bit or 64-bit versions of XP, Vista, and Windows 7
  • 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)

GeneStudio Pro Components

SeqVerter - sequence file format converter

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 thestand-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 - sequence alignment and phylogeny

Alignment editor - sequence alignment and phylogenyAlignment editor is a very convenient interface 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 - trace file assembly and editing

Contig editor - trace file assembly and editingContig 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.