/ 
Bio-BioStudio-2.00
River stage zero No dependents
/ BS_ChromosomeSegmentationPlanner.pl

NAME

 BS_ChromosomeSegmentationPlanner.pl

VERSION

Version 2.00

DESCRIPTION

 This utility proposes a set of restriction enzyme recognition site changes to
   a chromosome. The goal is to make the chromosome assemblable from
   multikilobase pieces called chunks, which in groups of roughly CHUNKNUM form
   larger pieces called megachunks. Megachunks end in special regions called
   InterSiteSequences (ISS), which consist of synthetic sequence, followed by a
   marker, followed by wild-type sequence, followed by a type IIB restriction
   enzyme recognition site.  The wild-type sequence targets the megachunk to
   its target chromosome for homologous recombination (thus wild type here can
   be any homologous chromosome, as long as gene order is the same). Megachunks
   alternate markers to allow a simple selection for successful integration.
   Markers should be defined in config/markers.

 No edits will be made, this utility merely proposes a plan for you to vet.
   If the plan meets your requirements, run BS_ChromosomeSegmenter to implement
   it.

ARGUMENTS

Required arguments:

 -C,  --CHROMOSOME : The chromosome to be modified
 --RESET  : Which list of restriction enzymes to use (defined in GeneDesign)
 -W,  --WTCHR  : The chromosome that will receive chunks (usually wildtype)
 -M,  --MARKERS : Comma separated list which will be alternately inserted
     into megachunk ISS sequences (must be defined in config/markers)

Optional arguments:

 -SC,  --SCOPE : [seg, chrom (def)] How much sequence will the edit
                 affect. seg requires STARTPOS and STOPPOS.
 -STA, --STARTPOS : The first base for analysis;ignored unless SCOPE = seg
 -STO, --STOPPOS  : The last base for analysis;ignored unless SCOPE = seg
 --CHUNKLENMIN : The minimum size for chunks (default 6000 bp)
 --CHUNKLENMAX : The maximum size for chunks (default 9920 bp)
 --CHUNKNUM : The target number of chunks per megachunk (default 4)
 --CHUNKNUMMIN : The minimum number of chunks per megachunk (default 3)
 --CHUNKNUMMAX : The maximum number of chunks per megachunk (default 5)
 --CHUNKOLAP : The number of bases each chunk must overlap (default 40)
 --ISSMIN : Minimum size of the homologous intersite sequence (default 900)
 --ISSMAX : Maximum size of the homologous intersite sequence (default 1500)
 --FIRSTLETTER : The first letter to assign a megachunk (default 'A')
 -FP, --FPUTRPADDING : No edit zone upstream of the five prime end of
           essential/fast growth genes when no UTR is annotated (default 500)
 -TP, --TPUTRPADDING : No edit zone downstream of the three prime end of
           essential/fast growth genes when no UTR is annotated (default 100)
 -L, --LASTMARKER : Which marker should be the last marker inserted (must be
           defined in config/markers)
 --REDOREDB : Force recreation of the restriction enzyme database. Useful if
           the chromosome sequence or the chunk size parameters change between
           uses of the Segmentation Planner
 -h,   --help : Display this message

COPYRIGHT 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.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.