EnglishFrenchSpanish

OnWorks favicon

dotter - Online in the Cloud

Run dotter in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command dotter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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.

Use dotter online using onworks.net services


Ad


Ad