No need to go through the TiledImage layer for this, either: we could generate the dotplot tiles independently, direct from sequence.

Simple tracks could just show dotplots a la dotlet. Or dotter (Erik Sonnhamer's cool X utility with nice, responsive contrast widget.... sadly don't think javascript is up to this!). More advanced tracks could show posterior probabilities for local direct repeats, inverted repeats and stem-loop structures, using various grammars.

-- IanHolmes - 28 Feb 2006

The program dottrack in dart/src/gfx now creates dotplot tracks, conveniently broken into tiles.

Type cd dart/src/gfx; make dottrack

Binary is placed in dart/bin. Type dottrack -h for help.

Basic usage is dottrack sequencefile.fasta but try also -log 5 for progress logging.

Currently does not do less than one base per pixel, i.e. super zoomed-in view (but can do more than one base/pixel, i.e. zoomed-out).

Should be pretty fast I think

For reference, at one-base-per-pixel, pixel intensity at is where for "forward track" and (where is complement of ) for "reverse track".

Some contrast issues. Hard to spot repeats. Should be averaging over diagonals, not square neighborhoods. Fix this!

-- IanHolmes - 11 Mar 2006