Introduction

Welcome to Vitasoft's home page.  This web site is setup to help users of DNAScriptor. It is maintained by Vitasoft Associates to provide users with current information, feedback and useful downloads that they can use with the program.  Visitors are welcome to view this site to understand what DNAScriptor and its associated language DNAScript does.  This site is not meant to be a source of information for DNA/Protein sequence analysis or other related programs.  A basic knowledge of molecular biology and DNA/Protein sequence analysis is assumed.

Our Mission

Our mission is to provide scientists with new tools to analyze and manipulate DNA and protein sequence information.  Our focus is to concentrate on software niches not already filled by others with the hope that we can complement rather than provide "me too" software products. For this reason we weight greatly user feedback so we can continue to evolve and improve our software.  

DNAScriptor is our first product.  The program has most of the features found in modern sequence analysis software, but its major contribution is that it provides a simple script drive language called DNAScript  that a allows the user to explore sequence analysis concepts in a generalized program mode.

DNAScriptor

DNAScriptor is a program in which a user can test and review DNA or protein sequence analysis concepts either manually; or through program functions, in a way that is generalized and flexible.  To support this functionality, DNAScriptor has two modes of operation:

  • Manual Mode:  This  mode allows the user to manually direct, one-step-at-a-time, the manipulation and analysis of DNA or protein sequences in special sequence display windows. This mode of operation is quite similar to many other sequence analysis programs. A description of individual sub-sections of this mode of operation can be found in the table below. Please click on the appropriate section for further information on that topic.

   Topic    Description
Introduction Modes of Operation, System Requirements, Installation, Registration.
Main Menu Commands File I/O, Database Configurations, Compiler Command, Help Commands.
Main Toolbar  Commands File Compression, Sequence Editing, FTP, Database Access,  E-Mail, Compiler.
Tools Toolbar Commands Seq Views, Seq Editing, Seq Searching,  Seq Downloads, Seq Alignments.
Homology / Alignment Tool Using The Show Homology / Alignment Tool.
NIH Blast Analysis Tool Utilizes NIH Blast public domain internet servers to analyze sequence data.
DNAScriptor's Compiler Running DNAScriptor in DNAScript Mode, A simple example.
Accessing Internet Databases Accessing GENBANK and EMBL Databases
Sequence Formats Sequence File Formats, Sequence Folders, Sequence Numbering

 

  • Program Mode:  This  mode allows the user to use a program language to automate the manipulation and analysis of DNA or protein sequences. This is done using a language we call “DNAScript”.  DNAScript is a general purpose, “Java Script like” interpreted programming language with rudimentary object-orientated functions to load, examine, and manipulate DNA and protein sequence data. Syntactically the core language resembles C, C++ and JavaScript. A programmer familiar with these languages should have no trouble with DNAScripts core constructs such as if statements, the while loop, for statements and operators like &&. Every effort was made in developing DNAScript to maintain consistent language syntax and to allow for future language developments. Click on DNAScript Introduction to get an overview of the language and see a few simple examples. The language functions can be divided into the following main groups:-

  Topic   Description
Sequence Manipulation Functions  The sequence manipulation functions are some of the most used functions in DNAScripts. They are characterized as those functions that load, query, manipulate print or save sequences as a whole.
Nucleotide and DNA Specific Functions  These functions are specific for DNA sequences. They have their counterpart protein specific functions. They are characterized by being those functions that allow the direct query and manipulate of nucleotides within a DNA sequence
Amino Acid and Protein Functions These functions are specific for protein sequences. They have their counterpart DNA specific functions. They are characterized by being those functions that allow the direct query and manipulate of amino acids within a protein sequence
Sequence View Functions These functions are used to view a sequence window.  They can be used for protein and DNA sequence windows.
Highlighted Region Functions These functions are used to select and modify a highlighted region within a sequence. They can be used for protein and DNA sequences.
Sequence Translation Functions These functions are used with DNA sequences to select, modify and display sequence translation results.
Sequence Buffer and String Functions  These functions are used to transfer sequences to and from sequence buffers or character strings.
Bookmark Functions  These functions are used to set “bookmarks” within a sequence. Such bookmarks allow the positioning within a sequence of  site specific information about a sub-sequence and its subsequent recall and display.
Sub-Sequence Search Functions  These functions are used to search for sub-sequences or sequence patterns within a sequence.
Internet Access Functions These functions are used to download and upload data from Internet URL sites.
File Compression Functions  These functions are used to compress or decompress file data. While they can be applied to any type of file, but are optimized for DNA and protein sequence files.
File and File Folder Functions  These common functions are used to obtain or set information about files stored on the users disk storage medium. Their use should be straightforward to most programmers and will be described as a group.
Special Sequence Functions  These specialized functions do not fall clearly into any of the previous categories and are given a section of their own.
Sequence Alignment Functions These functions deal with sequence alignments and the comparison of sequences with each other.
Input and Output Functions These functions deal the display of DNAScript data output, the control of the DNAScriptor compiler engine, or with the DNAScript dialog box itself.
Core DNAScript Functions  These are the core functions, rules, keywords and constants used by DNAScript.

 

Both of these modes of operation have many sub-components and features that will require practice on the part of the user to fully utilize their capabilities.  In particular, the DNAScript language is designed to be upward expandable, consistent in its function passing parameters to allow its general adaptation as a language for investigations to analyze sequence information.  Exchange and publication of DNAScript programs is encouraged.  The current language functions and syntax are defined in detail in the manual “DNAScript, a Programming Language” supplied with the program.

For all practical purposes, there is no limit to the size of the sequence that can be displayed or manipulated within DNAScriptor.  For example, the user can see “on the fly”, a scrollable display of restriction enzyme sites anywhere within a one million nucleotide long sequence.  This capability to handle large sequences is achieved through utilizing the full extend of modern 32-bit memory addressing methods and “multi-threaded” function programming.  Likewise, there is no limit to the number of sequences that can be concurrently opened and processed by DNAScriptor, although most desktop displays will limit this to less than about 20.

DNAScriptor includes the following printed and online documentation:

  • The DNAScriptor User Guide contains complete instructions for using all commands and features.

  • The DNAScript Language User Guide contains a complete description of all script function commands and examples of their use.

  • Online Help initiated from the program menu containing summary information in both User Guides.

Order Information

Orders for DNAScriptor must be associated with an institutional or company purchase order number (PO Number) along with other information.  A complete order form is provided here and must be filled out.  Direct orders will include the complete registered program an a CD as well as a complete set of manuals (300 pages).
A free trial version of DNAScriptor can be downloaded from this web site by clicking on this download button.  This is the full and complete version of DNAScriptor complete with example sequence and DNAScript files.  It consists of one large file (11Mgs) which will install the program on your computer. If required the program can later be easily uninstalled using the standard Microsoft uninstall program in your Windows control panel folder.  On certain network systems you may have to have System Administrator privileges to install the program.

 

 

This trial version of DNAScriptor will function for 3 months. It can later be upgraded to a registered licensed copy of the program from within the trial version of the program itself without any loss of configuration information etc. 

Once a order is received by Vitasoft as described above, a license key will be sent to you by e-mail to activate the license on the program. This will allow the program to run indefinitely on your computer.  Please note no support can be provided for trial versions of the program.

Note the program requires Microsoft Windows 95, 98 (or later) to operate. Windows 2000 or later is highly recommended. The program also requires that the Microsoft Internet Explorer Web Browser (v3.0 or later) reside on your computer. Internet Explorer does not have to be your default browser it just has to be resident on your computer. This is because the program utilizes certain .DLL's from the Explorer for Internet access. Normally these modules are installed when Windows 98 is first installed on your computer.

 

Contact Information

The best way to get in contact with us is by e-mail (see below).

Telephone  
925-964-9093
 
FAX   
925-964-9093
Postal address    
                Vitasoft Associates,
                3839 Cottonwood Drive
                Danville CA 94506
 
Electronic mail 
General Information: info@vitasoft.org