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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 |