DNA Strider (longish)

Harry Mangalam mangalam at SALK-SC2.SDSC.EDU
Thu Mar 18 12:34:24 EST 1993


>        I am trying to find out a)if there is a version of the DNA analysis
>program DNA Strider later than 1.1 and b) if so, how it differs from 
>version 1.1. Any information would be helpful. Thanks.

   Version 1.2 is the latest, is still $200 (if you didn't pay for 1.1) and
does a few more things.  Here's a bit from a rolling review.


- DNA Strider - One of the very few for-pay DNA analysis program that I can
unhesitatingly recommend. For $200, you can't buy more program. It can't
draw pretty pictures by reading Genbank Feature tables (but if it's already
in Genbank, most scientists I know aren't interested in the sequence per
se, but what can be done with it, and if you modify it, then the
annotations don't coincide, so you still have to draw the picture yourself
anyway). Strider can output its graphics in PICT form, so that they import
smoothly into drawing programs like Canvas.  It doesn't pretend to predict
secondary or (God forbid) tertiary structure. It does not support color. It
doesn't speak to you in multiple voices. What it does do, though, it does
incredibly fast. I've only seen ONE program that comes close to Strider for
speed in restriction mapping, and the screen output, while perhaps a little
spare (in the best Edward Tufte tradition) is _useful_! It's interface is
simple and smooth and easy to do real work with. 
   It will do some limited protein analysis, such as hydrophobicity, and
acid/base prediction, and the latest version (1.2) includes the ability to
do some primer analysis and Diagonal comparisons (much like DottyPlot).
Also, when you paste sequence into a Strider window, it intelligently
strips spaces, numbers, etc., allowing you to add sequences from nonStrider
formats relatively easily. Strider does not allow you to analyze more than
32.5K bases at a time, a nasty fault in my view and like all of the
commercial packages, doesn't allow you to add your own routines. 
   DNA Strider is available only from its author Christian Marck at the
following address:

Dr. Christian Marck
Service de Biochimie et de Genetique Moleculaire
Bat. 142 Centre d'Etudes de Saclay
91191 GIF-SUR-YVETTE      CEDEX        FRANCE
fax: (33 1) 69 08 47 12

(warning: he has been known to be slow in responding to correspondence not
containing cheques in the amount of US$200.  A Dr. Aral
(URA1335%frciti51.bitnet) reports that he now wants $250, but the "About
DNA Strider" window in 1.2 still reports $200; in any event, contact him
first).

Some timing data:


Timing Charts:

   The following times were obtained using MacIIfx (40Mhz 68030, 68882 fpu,
8 MB RAM, 507MB Fujitsu HD, System 6.0.5, 19" E-machines color monitor).  
   Times are also listed for DNA Strider using a Mac (MacSE, 8 Mhz 68000,
no fpu, 2.5 MB RAM, 40 MB CMS HD (Seagate mechanism), system 6.0.5) and a
MacIIci (25MHz 68030+68882, 8MB RAM, 105 MB HD (Conner LPS mechanism).  The
times were measured to the nearest half second using Douglas Adams'
instrument of societal dissolution, the digital watch. The sequence was
32.5 kb of lambda, the largest amount of sequence that Strider can handle
in one window.  The other programs can, unless noted, handle more sequence,
although with varying facility. Square brackets indicate an explanatory
note or additional information listed at bottom.


Program         Time to Restriction             Restriction     6 Frame 
                        Load            Map - Text           Map - Graphic 
    ORF Map

DNA Strider 1.2 2.5[1]  3.5/8.5[2]              1                       1
 (Mac SE)               19.2            42/1'43"                5.5        
            8
 (MacIIci)              8               9.5/17          1.5                
    3.5

MacVector 3.5   6               45/32[3]                29                 
    4[4]
                        
Geneworks 2.0   14              14/27[5]                18.5               
    4.5
(Demo)
DNAsis 1.0              5               10 Minutes[6]   [7]                
    38[8]
(Demo)

MacMolly Tetra  3.5             10.5[10]                [10]               
    12.5    
Analyze [9]

Sequencher              10              [11]                    3[11]      
            n/a
(Demo)

SeqApp (rel 2)  5               42[12]          [12]                    [12]
SeqApp (rel 3)  ?               ?[12.5]         [12.5]          [12.5]

DNASTAR Mac             10              4.5[13]         16                 
    4.5[13]
(MapDraw)

[1] At startup, Strider reads in and recalculates the hash table for it's
Restriction Enzyme library, an unnecessary waste of time, especially for
slower Macs.  This should really be made optional.
[2] Times are for "Restriction Map"/"Complete Restriction Map"; the latter
not only displays the textual restriction map, but all the enzyme sites
sorted by number and location of cuts. (170 enzymes)
[3] After 45", the program stopped with the error "too many sites"; after
<10 sites were selected, it completed in 32". (163 enzymes)
[4] MacVector can find ORFs by defining an ORF in a number of ways
including Ficketts Method.  I used the default ORF which looks for ORFs
beginning with an atg and ending with a stop, with a minimum translation of
25 aas.
[5] 14" for all 100 enzymes; 27" for those that cut <=2 times (the default).
[6] DNAsis could not import the text file of sequence and when I tried to
cut and paste the sequence into a "new" window, it reported a number of
invalid residues which it then stripped out, leaving the sequence about 400
nt short (there were no ambiguous nt in the sequence), so I pasted in the
missing # of nt from the same sequence.  I did not wait for the restriction
to complete; the program throws up a "remaining" thermometer and when it
hit 15%, I stopped it and did the math.  DNASIS can show either actual site
cleavage or use the 5' end of the recognition sequence (as Strider does);
it takes the same time either way. (247 enzymes; a contributing factor)
[7] I could not determine how to make DNAsis give me a graphic map without
modifying the enzyme file.
[8] DNAsis not only gives you an ORF map, but also includes a ORF position
table.
[9] Tetra comes in multiple modules; Analyze is the module that performs
the restriction and translation functions.
[10] The restriction enzyme selection process  is quite flexible, allowing
you to select or deselect by # of bases in the recognition site or by
overhang (but not by number of times of cutting).  After 10.5 minutes, the
first part of the screen appeared then an irreversible memory error
occurred.  After rebooting, I selected only 6 cutters and after 1 minute
the list had only gotten through the enzymes starting with "A", so I
canceled the digest; the typical Mac 'cancel' ("command" + ".") works
smoothly and does not kill the application. (324 enzymes).
[11] The Sequencher demo comes with only 21 enzymes entered in its
database, a strange omission, but Ver 1.0 comes with 59, still many less
than the norm. 
[12] No doubt a function of it's 'alpha' test status, SeqApp has some
quirks.  Despite it's incorporation of READSEQ, it was not able to smoothly
import the 32.5 kb sequence file and when I tried to copy/paste it into a
'new' window, the sequence could be pasted, but it was not 'intelligently
pasted' as it would have been in Strider - i.e. uneven lines, incomplete
numbering, and most bizarrely, no sequence showing up in the multiple
sequence window.  The sequence name was there and when selected again, the
sequence would appear in the editing window (still unevenly formatted, but
with the correct numbering), but I could not get it to show up in the
multiple sequence window.  After 42", the text window appeared showing the
enzyme cut sites, but I was unable to make the complete text sequence
window appear.  SeqApp does not support (yet?) graphic maps, and the
translation is supposed to show up underneath the text sequence, but
doesn't. (189 enzymes)
[13] I was astonished at how fast DNASTAR was able to produce the initial
map, including the sequence, complement, all restriction sites (146
enzymes), and 3 letter translations in all 6 frames (hence the same value
for the ORF map), any and all of which can be modified or removed using a
single easy-to-understand menu.  It, like a number of other programs has
screen sensing so that it will expand the window to full size initially. 
This may be annoying, because it obscures the rest of your screen.



If you want more specifics, shout.
Harry






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