Harry Mangalam <mangalam at home.com> writes:
> Is there an easy way to mask enzymes for possible Dam or Dcm methylase
> interference in 'map' or 'mapplot' or any other GCG app?
You would need to know the sensitivity of each enzyme to each specific
methylation. REBASE has the corresponding methylases for the enzymes
(where known), but if the Dam or Dcm sites overlap another enzyme
target, or if the correspoonding methylase makes a different
modification, there is no guide to what effect this could have.
You could check REBASE for methylases with the exact same target as
Dam and Dcm but it would not be complete. For example, EcoRII should
be inhibited by Dcm as the EcoRII methylase has the same product as
Dcm. Similarly, MboI should be inhibited by Dam.
We have a restrict program in EMBOSS which we would be happy to modify
if anyone can provide data for interference by other methylations.
Examples (REBASE in bairoch format):
Dcm methylase:
==============
ID M.EcoDcm
ET M
AC RB00004;
OS Escherichia coli K-12
PT EcoRII
RS CCWGG, ?;
MS 2(5mC);
//
MboI and methylase:
===================
ID MboI
ET R2
AC RB00095;
OS Moraxella bovis
PT MboI
RS GATC, 0;
//
ID M.MboIA
ET M2
AC RB03283;
OS Moraxella bovis
PT MboI
RS GATC, ?;
MS 2(6mA);
//
ID M.MboIB
ET M2
AC RB03284;
OS Moraxella bovis
PT MboI
RS GATC, ?;
MS 2(6mA);
//
Dam methylase:
==============
ID M.EcoDam
ET M
AC RB00014;
OS Escherichia coli K-12
PT MboI
RS GATC, ?;
MS 2(6mA);
//
EcoRII and methylase:
=====================
ID EcoRII
ET R2
AC RB00006;
OS Escherichia coli R245
PT EcoRII
RS CCWGG, 0;
//
ID M.EcoRII
ET M2
AC RB0000
OS Escherichia coli R245
PT EcoRII
RS CCWGG, ?;
MS 2(5mC);
//
--
----------------------------------------------------------------------
Peter Rice | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/
