Silent mutation software

Joe Smith jes at presto.med.upenn.edu
Thu Oct 31 15:59:32 EST 1996


In article
<Pine.SGI.3.94.961029194307.352B-100000 at leonardo.ls.huji.ac.il>
yoramg2 at LEONARDO.LS.HUJI.AC.IL (Yoram Gerchman) writes:

   I'm looking for a program that can find silent restriction sites. I have
   Silmut, but it limited to 100 enzymes that are 6-cutters.

Is this something generally needed?  I've seen two requests here in
the last month.

I recently wrote a Perl script to do this.  It's not fancy but we've
found it useful.  It works best on Unix or Linux but I've also run it
under MacPerl and it shoul work on just about any Perl platform.  I've
attached a sample run at the end of this message to give you a feel
for what it does.

I'm reluctant to make it public until it's had wider testing.  If
anyone is interested in testing it and giving me some feedback, email
me and I'll send it.

<Joe
---
 Joe Smith
 University of Pennsylvania                   jes at presto.med.upenn.edu
 Department of Physiology
 Philadelphia, PA 19104

---- begin sample run ---------------------------------------------------
presto$ cat ~/seq/azip.pep | ./reprot.perl commpro.609
# reprot.perl v0.2 1Oct96 JES
# Searching 'AZIP' (30aa)
#  against enzyme list 'commpro.609'
#  (all enzymes)
     1 BbvI.2(AQL), DdeI.1(AQ),
       EspI.0(AQL), Fnu4HI.2(AQL),
       HhaI.0(AQ), TseI.2(AQL)
     2 AluI.1(QL), BsrI.2(QLE),
       CviJI.1(QL), MfeI.0(QL),
       NspBII.0(QL), PvuII.0(QL),
       TspEI.1(QL)
     3 AvaI.0(LE), GsuI.0(LE),
       MaeI.0(LE), TaqI.1(LE),
       XhoI.0(LE)
     6 AluI.1(EL), BbvI~.2(ELQ),
       CviJI.1(EL), Fnu4HI.2(ELQ),
       HgiAI.0(EL), HgiJII.0(EL),
       MaeIII.2(ELQ),
       MwoI.2(ELQAL), SacI.0(EL),
       SduI.0(EL), TseI.2(ELQ),
       TspEI.1(EL)
     7 BsiYI.2(LQALE),
       Cac8I.2(LQA), Eco57I~.0(LQ),
       EcoRII.2(LQA), GsuI~.0(LQ),
       PflMI.2(LQALE), PstI.0(LQ),
       ScrFI.2(LQA), SfeI.0(LQ)
     8 AluI.2(QA), AlwNI.0(QAL),
       AsuI.2(QAL), CviJI.2(QA),
       DraII.1(QAL),
       Eco47III.2(QAL),
       HaeII.2(QAL), HaeIII.2(QA),
       HindIII.1(QAL), StuI.1(QAL)
     9 BsiYI.2(ALEKE), BsrI.2(ALE),
       DdeI.2(ALE), EcoNI.2(ALEKE),
       EcoRII.2(ALE), HhaI.0(AL),
       MnlI.2(AL), ScrFI.2(ALE),
       SecI.1(ALE), StyI.1(ALE),
       XbaI.2(ALE)
    10 AvaI.0(LE), GsuI.0(LE),
       MaeI.0(LE), TaqI.1(LE),
       XhoI.0(LE)
    13 BsmI.2(ENA)
    14 FnuDII.2(NA), MstI.2(NAQ)
    15 BbvI.2(AQL), DdeI.1(AQ),
       EspI.0(AQL), Fnu4HI.2(AQL),
       HhaI.0(AQ), TseI.2(AQL)
    16 AluI.1(QL), BsrI.2(QLE),
       CviJI.1(QL), MfeI.0(QL),
       NspBII.0(QL), PvuII.0(QL),
       TspEI.1(QL)
    17 AvaI.0(LE), GsuI.0(LE),
       MaeI.0(LE), TaqI.1(LE),
       XhoI.0(LE)
    20 AluI.1(EL), BbvI~.2(ELQ),
       CviJI.1(EL), Fnu4HI.2(ELQ),
       HgiAI.0(EL), HgiJII.0(EL),
       MaeIII.2(ELQ),
       MwoI.2(ELQAL), SacI.0(EL),
       SduI.0(EL), TseI.2(ELQ),
       TspEI.1(EL)
    21 BsiYI.2(LQALE),
       Cac8I.2(LQA), Eco57I~.0(LQ),
       EcoRII.2(LQA), GsuI~.0(LQ),
       PflMI.2(LQALE), PstI.0(LQ),
       ScrFI.2(LQA), SfeI.0(LQ)
    22 AluI.2(QA), AlwNI.0(QAL),
       AsuI.2(QAL), CviJI.2(QA),
       DraII.1(QAL),
       Eco47III.2(QAL),
       HaeII.2(QAL), HaeIII.2(QA),
       HindIII.1(QAL), StuI.1(QAL)
    23 BsiYI.2(ALEKE), BsrI.2(ALE),
       DdeI.2(ALE), EcoNI.2(ALEKE),
       EcoRII.2(ALE), HhaI.0(AL),
       MnlI.2(AL), ScrFI.2(ALE),
       SecI.1(ALE), StyI.1(ALE),
       XbaI.2(ALE)
    24 AvaI.0(LE), GsuI.0(LE),
       MaeI.0(LE), TaqI.1(LE),
       XhoI.0(LE)
    27 AluI.1(EL), Cac8I.2(ELA),
       CviJI.1(EL), HgiAI.0(EL),
       HgiJII.0(EL), NheI.2(ELA),
       SacI.0(EL), SduI.0(EL),
       TspEI.1(EL)
    28 AluI.2(LA), AsuI.2(LAQ),
       CviJI.2(LA), FnuDII.2(LA),
       HaeIII.2(LA), MaeI.0(LA),
       MstI.2(LAQ)
    29 DdeI.1(AQ), HhaI.0(AQ)
------------------------------------------------------------
-- 
 Joe Smith
 University of Pennsylvania                   jes at presto.med.upenn.edu
 Department of Physiology
 Philadelphia, PA 19104




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