dotter(1)
Sequence dotplots with image enhancement tools.
SYNOPSIS
dotter [options] <horizontal_sequence> <vertical_sequence> [X options]
DESCRIPTION
-
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.
- Allowed types:
-
-
Protein - Protein
DNA - DNA
DNA - Protein
-
Options:
- -b <file>
-
Batch mode, write dotplot to <file>
- -l <file>
-
Load dotplot from <file>
- -m <float>
-
Memory usage limit in Mb (default 0.5)
- -z <int>
-
Set zoom (compression) factor
- -p <int>
-
Set pixel factor manually (ratio pixelvalue/score)
- -W <int>
-
Set sliding window size. (K => Karlin/Altschul estimate)
- -M <file>
-
Read in score matrix from <file> (Blast format; Default: Blosum62).
- -F <file>
-
Read in sequences and data from <file> (replaces sequencefiles).
- -f <file>
-
Read feature segments from <file>
- -H
-
Do not calculate dotplot at startup.
- -R
-
Reversed Greyramp tool at start.
- -r
-
Reverse and complement horizontal_sequence (DNA vs Protein)
- -D
-
Don't display mirror image in self comparisons
- -w
-
For DNA: horizontal_sequence top strand only (Watson)
- -c
-
For DNA: horizontal_sequence bottom strand only (Crick)
- -q <int>
-
Horizontal_sequence offset
- -s <int>
-
Vertical_sequence offset
-
Some X options:
-acefont <font> Main font.
-font <font> Menu font.
