enzymes files

Peter Rice pmr at sanger.ac.uk
Tue Dec 12 04:57:12 EST 1995

In article <951211131757.ZM2127 at si05.IRCM.UMontreal.CA> duhaimj at IRCM.UMontreal.CA ("SI-Johanne Duhaime") writes:
>>In article <Pine.SOL.3.91.951208161728.28216A-100000 at terre>, 
>duhaimj at IRCM.UMontreal.CA (SI-Johanne Duhaime) writes:
>>>I would like to know if there is any sites where I can find enzymes files
>>>classified by the number of bases involved in the recognition site.
>>>With GCG you can map a sequence with the enzymes that recognize 6 or more
>>>bases. But if I want to find enzymes that recognize exactly 8 bases and do 
>>>not want to scan all the results, what do I do? 
>I am afraid I was not clear in this message.  What I want is a set of 
>files that would contains individualy enzymes that would cut a same 
>number of bases in a recognisation sites (could be 5 or 6 or xbases). 
>Or it might be any other way to do the following: 
>where cut enzymes with 5 bases longs recognition sites; where cut 
>enzymes with 6 bases recognition sites;etc.
>I could myself create files with those enzymes by edititing of 
>enzyme.dat but I was wondering if this was already existing on the www 
>by exemple.

Nice suggestion. I have included this in EGCG 8.1 (due soon) in the
MapSelect program, which allows users to select enzymes and writes a new
enzyme local data file.

Here are the results for 8-cutters (note that this includes some cases
where ambiguous base codes are counted - R and Y for example - but does
not count the positions where any base (N or X) is allowed). Both minimum
and maximum base counts are allowed (-MINBASE=5 -MAXBASE=5 for example
to get the 5 cutters) :

MAPSELECT enzyme pattern file     December 12, 1995 09:50

AscI        2       GG'CGCG_CC            4       ! 
FseI        6       GG_CCGG'CC            -4      ! 
NotI        2       GC'GGCC_GC            4       ! 
PacI        5       TTA_AT'TAA            -2      ! 
PmeI        4       GTTT'AAAC             0       ! 
SfiI        8       GGCCn_nnn'nGGCC       -3      ! 
SgfI        5       GCG_AT'CGC            -2      ! 
SgrAI       2       Cr'CCGG_yG            4       ! 
SrfI        4       GCCC'GGGC             0       ! 
Sse8387I    6       CC_TGCA'GG            -4      ! 
SwaI        4       ATTT'AAAT             0       ! 

Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr/   | England

More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net