DOTTER(1)

💖 NAME 💖

dotter — sequence dotplots with image enhancement tools ✨

🦋 DESCRIPTION 🦋

okay so bestie, Dotter makes sequence dotplots and it comes with image enhancement tools built in. it's giving "genomics but make it cute." 💅

here's the vibe of how you run it:

dotter [options] <horizontal_sequence> <vertical_sequence> [X options]

where <horizontal_sequence> and <vertical_sequence> are file names for FASTA files holding your two sequences. no cap, that's the whole ritual. 🎀

🌸 allowed sequence types 🌸

not every combo is allowed, so let's do a vibe check:

• Protein – Protein
• DNA – DNA
• DNA – Protein

✨ OPTIONS ✨

• -h, --help — show this usage information. the "help me bestie" button 🫶
• -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). yes, half a megabyte. she's frugal. 😭
• -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

💜 the credits (iykyk) 💜

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) 2010-2015: 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

🎀 AUTHOR 🎀

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶

and that's the whole page, bestie!! this little writeup is for dotter version 4.44.1, dated October 2017, and yes it's still the DOTTER(1) manual — go make some iconic dotplots, you've got this 💖✨🦋🌸💅