dotter − Sequence dotplots with image enhancement tools.
dotter [options] <horizontal_sequence> <vertical_sequence> [X options]
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. |
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−R |
Reversed Greyramp tool at start. |
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−r |
Reverse and complement horizontal_sequence (DNA vs Protein) |
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−D |
Don’t display mirror image in self comparisons |
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−w |
For DNA: horizontal_sequence top strand only (Watson) |
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−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.
http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.
Erik DOT Sonnhammer AT cgb DOT ki DOT se Version 3.1, compiled Jul 10 2010