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 !
--
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Peter Rice | Informatics Division
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