Hello,
>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:
http://www.enzim.hu/~tusi/restric/restenzyme.html
It uses a very simple table:
nwryhmksdacgt
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
www.enzim.hu/~ _/_/_/_/_/_/ _/ _/_/_/ _/
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