dotter: Sequence dotplots with image enhancement tools.

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

-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