NAME
dotter - Sequence dotplots with image enhancement tools
DESCRIPTION
-
Dotter - Sequence dotplots with image enhancement tools.
- Usage: dotter [options] <horizontal_sequence> <vertical_sequence>
-
[X options]
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Where <horizontal_sequence> and <vertical_sequence> are file names for FASTA files containing the two sequences.
- Allowed sequence types:
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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>
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Batch mode; export plot to PDF file <file>
-l <file>, --load
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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
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Set pixel factor manually (ratio pixelvalue/score)
-W <int>, --window-size
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Set sliding window size. (K => Karlin/Altschul estimate)
-M <file>, --matrix-file=<file>
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Read in score matrix from <file> (Blast format; Default: Blosum62).
-F <file>, --sequence-file
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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
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Reversed Greyramp tool at start.
-r, --reverse-horizontal
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Reverse and complement horizontal_sequence (if DNA)
-v, --reverse-vertical
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Reverse and complement vertical_sequence (if DNA)
-D, --disable-mirror
-
Don't display mirror image in self comparisons
-w, --watson-only
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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
--horizontal-type=p|d
-
Horizontal_sequence type ('p' for peptide or 'd' for DNA)
--vertical-type=p|d
-
Vertical_sequence type ('p' for peptide or 'd' for DNA)
--abbrev-title-on
-
Abbreviate window title prefixes
--abbrev-title-off
-
Do not abbreviate window title prefixes
--session_colour=<colour_str>
-
Set the background colour of the dotter window
--compiled
-
Show package compile date
--version
-
Show package version
-----
-
Written by Gemma Barson <[email protected]> Based on original code by Erik Sonnhammer <[email protected]>
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Reference: Sonnhammer ELL & Durbin R (1995). A dot-matrix program
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with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167(2):GC1-10.
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See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
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Copyright (c) 2010-2015: Genome Research Ltd. Dotter is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt
- Version 4.44.1
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14:27:56 Oct 19 2017
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.