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MAP routine ENZyme qualifier

Charles Bailey bailey at genetics.upenn.edu
Tue May 24 16:51:29 EST 1994


In article <1994May24.141718.171211 at eros.embl-heidelberg.de>, rice at embl-heidelberg.de (Peter Rice) writes:
> In article <01HC6TWV7M9S0018R8 at crcvms.unl.edu>, CSMITH at CRCVMS.UNL.EDU writes:
>> I am running a LOT of RE digest analyses with the MAP routine, using the same
>> set of 20 RE's. Inputing the abrevs for each of the enzymes either as the 
>> /ENZyme qualifier or as prompted from within the routine has been a tedious
>> task. To aleviate some of the manual work, I tried using a file list of the 
>> enzymes with the enzyme qualifier ... /ENZyme=@enzyme.list, but to no avail.
>> Is there a WORKABLE and/or BETTER way of inputing a list of RE's ?
> 
> This is one of the extensions included in the EGCG package. The MAPSELECT
> program is a version of MAP that writes a new enzyme file. You can then
> use this file with /ENZFILE=filename (note: it must be ENZFILE not ENZYME
> as in your example, otherwise MAP ignores it) in a later run of MAP.

If you want to do this using the vanilla GCG programs, you can also create a
custom enzyme file by simply copying the lines from GenRunData:Enzyme.Dat
describing the enzymes of interest to you into a new file.  Be sure to put a 
.. above the first entry (you can include any comments you like above the ..),
and then specify the new file using the /Data qualifier to any of the MAP*
programs.

For instance, here's a custom file I use frequently when designing ways to
subclone a piece of DNA.  It contains only those restriction enzymes with sites
in the polylinker or either pUC18/19 or pBlueScript.

PolyLink.Enz
  GCG enzyme data file for enzymes in polylinker of pUC18/19 or
  Stratagene pBlueScriptSK/KS

          Off            Over Com                        Commercial
Enzyme    Set  Site      Hang ment Isoschizomers         Source  ..
AccI       2 GT'mk_AC       2 !                          >ABEGIKMNOPRSUVX
ApaI       5 G_GGCC'C      -4 !                          >BEGIKMNOPRUVX
BamHI      1 G'GATC_C       4 !  BstI                    >ABEGIKMNOPRSUVX
BanII      5 G_rGCy'C      -4 !                          >EGIKMNOPRSUVX
BstXI      8 CCAn_nnnn'nTGG  -4 !                        >EGMNORUVX
ClaI       2 AT'CG_AT       2 !  BanIII                  >ABEGKMNPRSVX
DraII     2 rG'GnC_Cy       3 !  EcoO109I,PssI           >EGM
EagI      1 C'GGCC_G        4 !  Eco52I,XmaIII,EclXI     >N
EcoRI      1 G'AATT_C       4 !                          >ABEGIKMNOPRSUVX
EcoRV      3 GAT'ATC        0 !                          >ABEGIKMNOPRSUVX
HincII     3 GTy'rAC        0 !  HindII                  >ABEGIKNOPRSUVX
HindIII    1 A'AGCT_T       4 !                          >ABEGIKMNOPRSUVX
KpnI       5 G_GTAC'C      -4 !  Asp718I                 >ABEGIKMNOPRSUVX
NotI       2 GC'GGCC_GC     4 !                          >ABEGIKMNOPRSUVX
PstI       5 C_TGCA'G      -4 !                          >ABEGIKMNOPRSUVX
SacI      5 G_AGCT'C       -4 !  SstI                    >AEGIKMNOPRSUVX
SacII      4 CC_GC'GG      -2 !  MraI,SstII,KspI         >EINOPRUVX
SalI       1 G'TCGA_C       4 !                          >ABEGIKMNOPRSUVX
SmaI       3 CCC'GGG        0 !  Cfr9I,XmaI              >ABEGIKMNOPRSUVX
SpeI       1 A'CTAG_T       4 !                          >BEGKMNORSUX
SphI       5 G_CATG'C      -4 !  BbuI                    >ABEGIKMNOPRSUVX
XbaI       1 T'CTAG_A       4 !                          >ABEGIKMNOPRSUVX
XmaI      1 C'CCGG_G        4 !  Cfr9I,SmaI              >EINRVX
XhoI      1 C'TCGA_G        4 !  CcrI,PaeR7I,BstVI       >ABEGIKMNOPRSUVX

                    Regards,
                    Charles Bailey

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