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dotter - Sequence dotplots with image enhancement tools.

DOTTER:(1) General Commands Manual DOTTER:(1)

NAME

dotter - 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.

SEE ALSO

http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.

AUTHOR

Erik.Sonnhammer@cgb.ki.se Version 3.1, compiled Jul 10 2010
July 2010 Debian Sid