[BiO BB] Re: VectorNTI [BiO_Bulletin_Board digest, Vol 1 #186]

[Rick Westerman]

>. Does anyone have any comments to share about the Vector NTI suite
>offered by InforMax (http://www.informaxinc.com/solutions/)?  In
>particular, how does it fare in comparison to GCG?
>
>. I am wondering if the main selling part of this program is the
>integration between the various analysis tools (which I realize becomes a
>great time saver in a certain situations), which it appears to do a
>good job at.  However I am more interested in the performance of the
>algorithms more than anything.

    The algorithms are, of course, hidden from us but they seem to be 
standard ones.  There are only so many ways that a program can do enzyme 
cutting, multiple sequence alignment, etc. and generally these methods are 
published and, if coded properly, robust.  VNTI will also send your 
sequence to web sites if the site contains a unique algorithm.

     As for performance, I suspect my GHz PC running VNTI outperforms my 
Sun server at 400 MHz for most applications.  Of course I do not have the 
Genbank database on PC and so can't do local Blast searches.  VNTI simply 
sends your sequence to NCBI in order to do a Blast search.

    And that brings up the major limitation of VNTI: it generally works 
with one sequence at a time.   If a person wants to work with 100s of 
sequences then GCG (or other command-line oriented package) is the way to go.

    Please note that VNTI's support for the Mac is rather old.  The current 
PC version is 7; the Macs are stuck at version 5.3 until (if and when) 
Informax decides to develop for OS-10.

    VNTI is also expensive.  As an academic site we can purchase a 
site-wide GCG license for less than the price of two VNTI single-lab 
licenses.  There is a test copy of VNTI available so that you can try it 
out yourself.

    In summary we use both packages.  Some people really love VNTI -- it 
looks nice and helps visualize single sequencing processing -- while other 
people avoid it and get along with GCG and other server-based tools.

-- Rick

Rick Westerman
westerman at purdue.edu

Phone: (765) 494-0505                         FAX: (765) 496-7255
S049 WSLR bldg. Purdue Univ. W. Lafayette, IN 47907-1153

Bioinformatics specialist at the Genomics Initiative.
Part time system manager of Biochemistry department.

href="http://www.biochem.purdue.edu/~westerm"