dotter

detailed comparison of two genomic sequences

Description

Dotter is a graphical dot-matrix program for detailed comparison of two sequences.

* Every residue in one sequence is compared to every residue in the

other, and a matrix of scores is calculated.

* One sequence is plotted on the x-axis and the other on the y-axis.

* Noise is filtered out so that alignments appear as diagonal lines.

* Pairwise scores are averaged over a sliding window to make the score

matrix more intelligible.

* The averaged score matrix forms a three-dimensional landscape,

with the two sequences in two dimensions and the height of the

peaks in the third. This landscape is projected onto two

dimensions using a grey-scale image - the darker grey of a peak,

the higher the score is.

* The contrast and threshold of the grey-scale image can be adjusted

interactively, without having to recalculate the score matrix.

* An Alignment Tool is provided to examine the sequence alignment that

the grey-scale image represents.

* Known high-scoring pairs can be loaded from a GFF file and overlaid

onto the plot.

* Gene models can be loaded from GFF and displayed alongside the

relevant axis.

* Compare a sequence against itself to find internal repeats.

* Find overlaps between multiple sequences by making a dot-plot of all

sequences versus themselves.

* Run Dotter in batch mode to create large, time-consuming dot-plots as

a background process.

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