NAME
BS_GlobalREMarkup.plVERSION
Version 2.00DESCRIPTION
This utility creates an exhaustive database of restriction enzyme recognition
sites along a chromsome, both existing and potential.
Every intergenic sequence is parsed for existing recognition sites. Those that
are found are marked (i)mmutable; A suffix tree is created from all possible
6-frame translations of restriction enzyme recognition sites, such that each
node in the tree is an amino acid string that may be reverse translated to be
a recognition site. Every exonic sequence in the chromosome is then searched
with the suffix tree both for (e)xisting recognition sites and for sites
where a (p)otential recognition site could be introduced without changing the
protein sequence of the gene. As long as they occur within protein coding
genes, existing and potential recognition sites may be manipulated to yield
any of several different overhangs, all of which are computed by the
algorithm.
A score is assigned to every restriction enzyme site. The score is a function
of the log of the enzyme's price per unit, plus one tenth for each orf that
must be modified to make the enzyme unique within the range of the chunk
size, plus one half for each fast growth orf modified, plus one for each
essential orf modified.
Every extant site is indexed so that later in the design process, when
potential sites are considered, the number of sites that must be modified is
a known contribution to the cost. However, all potential sites that could
not be made unique under any circumstances are culled from the database,
with a window size that defaults to 2000 base pairs but may be defined by
the user.ARGUMENTS
Required arguments:
-CHR, --CHROMOSOME : The chromosome to be modifiedOptional arguments:
--REDOREDB : Whether or not to reform the RE database from scratch
-CU, --CULLINC : The width of the culling window
--RESET : Which list of restriction enzymes to use (default nonpal)
--CHUNKLENMIN : The minimum size of chunks to be designed (default 5000)
--CHUNKLENMAX : The maximum size of chunks to be designed (default 10000)
-h, --help : Display this messageCOPYRIGHT AND LICENSE
Copyright (c) 2013, BioStudio developers All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
* The names of Johns Hopkins, the Joint Genome Institute, the Lawrence Berkeley National Laboratory, the Department of Energy, and the BioStudio developers may not be used to endorse or promote products derived from this software without specific prior written permission.
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