A new DNA/Protein analysis software program. First looks.

John Monahan monahan at vitasoft.org
Fri Jun 8 05:11:26 EST 2001


Vitasoft Associates would like to let this specialized newsgroup be the first to know
about a new DNA/Protein analysis software program we have developed over the past few
years and will soon be launched to the molecular biology community. Hopefully this
will not be viewed as another "me too" sequence analysis program over the many other
excellent programs already available. The program is called "DNAScriptor".  What is
different about this program is that it is really two programs in one. The two modes
are:-

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. Amongst the commands are:-

DNA/Protein Sequence Views, Editing, Sub-sequence Searching,  Local Database Sequence
Analysis, Sequence Alignments, File Compression, FTP, Database Access,  E-Mail, Access
to NIH Blast/EMBL public domain internet servers to analyze sequence data etc.

Nothing real special here although the user will find the mode of display and data
manipulation to be simple, intuitive, very fast, and somewhat unique in the use of
mouse driven cursor commands.

The novel part of DNAScriptor is its second mode of operation:-

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 &&,||, etc. Every effort was made in developing
DNAScript to maintain consistent language syntax and to allow for future language
developments.

A "Hello World" example equivalent of the language would be:-

dna1 = LoadDNASeq("pBR322.seq");
ComplementSeq(dna1);
SaveSeqAs(dna1,"pBR322_complemented.seq");
CloseSeq(dna1);

If you are interested in finding out more about DNAScriptor please go to our web site
at www.vitasoft.org  A 3 month trial version of the program can be downloads from this
site.

Comments and suggestions are requested in order for us to appraise the product.





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