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DOTTER:

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 DOT Sonnhammer AT cgb DOT ki DOT se Version 3.1, compiled Jul 10 2010

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