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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