NAME

GD_Filter_Enzymes.pl

VERSION

Version 5.56

DESCRIPTION

Creates a list of restriction enzymes that meet optionally provided criteria.
Any criteria left blank will not be used to filter the results.

USAGE

List all enzymes that leave non-1bp overhangs and cut inside recognition seq:
      GD_Filter_Enzymes.pl --sticky 35 --cleavage in

List all enzymes that are available from NEB or Stratagene and are inactivated
at or below 60 deg and cost less than 50 cents a unit:
      GD_Filter_Enzymes.pl --vendor N,E --inactivation 60 --pricemax .5

List all enzymes that have at least 25% activity in NEB buffers 1 and 4 and
are indifferent to CpG methylation
      GD_Filter_Enzymes.pl --buffer NEB1=25,NEB4=25 --cpgsense indifferent

List all enzymes that exhibit star activity and are blocked or inhibited by
Dam methylation
      GD_Filter_Enzymes.pl --staractivity 1 --damsense blocked,inhibited

List all enzymes that may leave nonpalindromic overhangs (and those that
definitely do) and whose recognition sequences do not contain AT or TA
      GD_Filter_Enzymes.pl --palindromy pnon,nonpal --seqmaynothave AT,TA

ARGUMENTS

Optional arguments:

-h,   --help : Display this message
-enzymelist     : The name of an enzyme set to use in configuration, defaults
                  to standard_and_IIB
--sticky        : [1, 3, 5, b] What type of overhang is left by the enzyme
--palindromy    : [pal, pnon, nonpal] Is the overhang left by the enzyme
                  palindromic, potentially non-palindromic, or non-palindromic
--length        : How many bases long is the recognition site allowed to be,
                  accepts a comma separated list
--ambiguous     : [nonNonly OR ATCGonly] Are ambiguous bases allowed in the
                  recognition site. If yes to all, don't include this option
--inactivation  : Enzymes must be inactivated by at least this temperature
--incubation    : Enzymes must incubate at this temperature
--staractivity  : [1 OR 0] Enzymes with or without star activity
--cpgsense      : [blocked, inhibited, indifferent] Sensitivity to CpG
                  methylation
--damsense      : [blocked, inhibited, indifferent] Sensitivity to Dam
                  methylation
--dcmsense      : [blocked, inhibited, indifferent] Sensitivity to Dcm
                  methylation
--buffer        : List of buffer activity thresholds. NEB1=50,NEB2=50 means
                  enzymes must have at least 50% activity in NEB buffers 1 & 2
                  Other=50 will work for non NEB buffers
--pricemax      : The highest amount in dollars/unit an enzyme can cost
--seqmusthave   : List of sequences that must be found in the recognition site
--seqmaynothave : List of sequences that must not be in the recognition site
--vendor        : List of vendors that must stock the enzyme, using the
                  comma separated abbreviations:
                      B = Invitrogen
                      C = Minotech
                      E = Stratagene
                      F = Thermo Scientific Fermentas
                      I = SibEnzyme
                      J = Nippon Gene Co.
                      K = Takara
                      M = Roche Applied Science
                      N = New England Biolabs
                      O = Toyobo Technologies
                      Q = Molecular Biology Resources
                      R = Promega
                      S = Sigma Aldrich
                      U = Bangalore Genei
                      V = Vivantis
                      X = EURx
                      Y = CinnaGen