Preferred isoschizomer ?

[Eija Korpelainen]

Dear Fernan, Guy and others,

we have been looking into this problem with Alan and as he told you, the
embossre.equ -file is now made automatically. -preferred works (gives you
PstI instead of BspMAI) because the default value of -limit is true (this is
defined in the restrict.acd file). So if one is using a graphical interface
one has to tick both -preferred and -limit to get the right thing. This is
because in the code of restrict.c -preferred (called "equiv" in the code) is
considered only when -limit has been chosen. What the program actually does
is that it first limits to one isoschizomer and picks the alphabetically
first one (!), and then converts this to the prototype enzyme using the
embossre.equ file. The limiting step is performed by the function
embPatRestrictRestrict in embpat.c (in the nucleus directory).

The problem with the current set up is that the user doesn't know
that -limit and -preferred are interconnected. This could of course be
documented, but the easy fix would be to set the equiv boolean true in the
code and abolish the -preferred qualifier altogether. This way -limit would
give you automatically PstI, and -nolimit all isoschizomers.

As Guy pointed out, the problem with remap is that it does not take any
notice of the -preferred. This is simply because the code reads the value of
preferred (or equiv) but doesn't use it for anything. In other words, most
of remap.c code comes from Alan's restrict.c code, but the following
critical bit was accidentally left out.
if(equiv && limit)
{
value = ajTableGet(table,m->cod);
if (value)
ajStrAss(&m->cod,value);
}

I think it would be important to fix these problems because these are quite
central programs for molecular biologists and expensive projects like
transgenic design depend heavily on proper restriction maps.

Cheers,
Eija

_____________________________________________

Eija Korpelainen, Ph.D
Science Support/Biosciences
CSC - Center for Scientific Computing
P.O.Box 405, FIN-02101 Espoo, Finland
Phone    +358 9 457 2030
Mobile   +358 50 381 9726
Fax        +358 9 457 2302
E-Mail    Eija.Korpelainen at csc.fi
________________________________________________