Algorithm for Restriction Enzyme Analysis

Gabor E. Tusnady tusi at enzim.hu
Mon Jan 4 11:49:46 EST 1999


>Hi All,
>I am in trouble. I am developing an algorithm for restriction enzyme analysis
>but it is taking too long. The reason is because there are so many degenerate
>bases in the DNA sequence and thus it takes very long to analyze for all of
>them considering the possible combiantions they make. All the more the
>recognition sequence also have degenerate bases. Is there anybody out there to
>help me optimize the algorithm? Yes, there is. So thanking in advance to all
>those who respond.
>Ravi Gupta.
>Research Scholar

There is a little program, called restenzyme on the net:

It uses a very simple table:

ACGT n+++++++++++++
AT   w+++++++-++--+
GA   r+++-++++++-+-
CT   y++-+++-++-+-+
CAT  h+++++++++++-+
AC   m++++++-++++--
TG   k+++++-+++--++
CG   s+-+++++++-++-
GAT  d++++++++++-++
A    a+++-++--++---
C    c+--+++-+--+--
G    g+-+---+++--+-
T    t++-++-+-+---+

so if you have a degenerated sequence and degenerated recognition site of
the restriction enzymes, this table shows whether they can be the same.
For example the sequence:   ...acacnwk...
           the rec. site:   ...dynctyh...
characters from the table:  ...+++++++... 

thus the enzyme restricts this sequence, and you dont have to compare all
the combinations, only get the correspondeng matrix elements.

Best regards,
Gabor E. Tusnady
Institute of Enzymology

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