dotter1

Sequence dotplots with image enhancement tools

Overview

: 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

--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]>

: 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) 2010-2015: Genome Research Ltd. Dotter is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt

Version 4.44.1: 14:27:56 Oct 19 2017

Releases

7 releases since Debian 7 (Wheezy); the text changed 1 time.

--abbrev-title-off since Debian 10 (Buster); --abbrev-title-on since Debian 10 (Buster); --batch-export since Debian 10 (Buster); --batch-save since Debian 10 (Buster); --compiled since Debian 10 (Buster); --crick-only since Debian 10 (Buster); --disable-mirror since Debian 10 (Buster); --feature-file since Debian 10 (Buster); --help since Debian 10 (Buster); --horizontal-offset since Debian 10 (Buster); --horizontal-type since Debian 10 (Buster); --hsp-mode since Debian 10 (Buster); --load since Debian 10 (Buster); --matrix-file since Debian 10 (Buster); --memory-limit since Debian 10 (Buster); --pixel-factor since Debian 10 (Buster); --reverse-greyramp since Debian 10 (Buster); --reverse-horizontal since Debian 10 (Buster); --reverse-vertical since Debian 10 (Buster); --sequence-file since Debian 10 (Buster); --session_colour since Debian 10 (Buster); --version since Debian 10 (Buster); --vertical-offset since Debian 10 (Buster); --vertical-type since Debian 10 (Buster); --watson-only since Debian 10 (Buster); --window-size since Debian 10 (Buster); --zoom since Debian 10 (Buster); -e since Debian 10 (Buster); -h since Debian 10 (Buster); -v since Debian 10 (Buster).