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Dotter - Sequence dotplots with image enhancement tools.
Usage: dotter [options] <horizontal_sequence> <vertical_sequence> [X options]
Where <horizontal_sequence> and <vertical_sequence> are file names for FASTA files
containing the two sequences.
Allowed sequence types: Protein - Protein
DNA - DNA
DNA - Protein
Options:
-h, --help
Show this usage information
-b <file>, --batch-save=<file>
Batch mode; save dot matrix to <file>
-e <file>, --batch-export=<file>
Batch mode; export plot to PDF file <file>
-l <file>, --load
Load dot matrix from <file>
-m <float>, --memory-limit=<float>
Memory usage limit in Mb (default 0.5)
-z <int>, --zoom
Set zoom (compression) factor
-p <int>, --pixel-factor
Set pixel factor manually (ratio pixelvalue/score)
-W <int>, --window-size
Set sliding window size. (K => Karlin/Altschul estimate)
-M <file>, --matrix-file=<file>
Read in score matrix from <file> (Blast format; Default: Blosum62).
-F <file>, --sequence-file
Read in sequences and data from <file> (replaces sequencefiles).
-f <file>, --feature-file
Read feature segments from <file>
-H, --hsp-mode
Do not calculate dotplot at startup.
-R, --reverse-greyramp
Reversed Greyramp tool at start.
-r, --reverse-horizontal
Reverse and complement horizontal_sequence (if DNA)
-v, --reverse-vertical
Reverse and complement vertical_sequence (if DNA)
-D, --disable-mirror
Don't display mirror image in self comparisons
-w, --watson-only
For DNA: horizontal_sequence top strand only (Watson)
-c, --crick-only
For DNA: horizontal_sequence bottom strand only (Crick)
-q <int>, --horizontal-offset=<int>
Horizontal_sequence offset
-s <int>, --vertical-offset=<int>
Vertical_sequence offset
--compiled
Show package compile date
--version
Show package version
-----
Written by Gemma Barson <gb10@sanger.ac.uk>
Based on original code by Erik Sonnhammer <Erik.Sonnhammer@sbc.su.se>
Reference: Sonnhammer ELL & Durbin R (1995). A dot-matrix program
with dynamic threshold control suited for genomic DNA and protein
sequence analysis. Gene 167(2):GC1-10.
See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
Copyright (c) 2010-2011: Genome Research Ltd.
Dotter is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt
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