Ensembl DotterView
Introduction
Ensembl 'DotterView' is based on 'Dotter' (1). This program compares two DNA sequences by dot matrix analysis and displays regions of potential homology. Optionally, alignments of high-scoring segment pairs (HSPs) can be listed.
When 'DotterView' is reached via a conserved block from an Ensembl 'ContigView' page, 10 kb genome sequence from each species centred on the match are compared. The sequence from the focus species (e.g. human) is represented on the vertical axis, while the sequence of the 'matching' species (e.g. mouse) is represented on the horizontal axis.
In regions where the two sequences are similar to each other, a row of dots will run diagonally across the display.
'DotterView' operates with a sliding window of 20 bp size. A minimum threshold similarity can be selected clicking into the 'Greyscale Map' near the bottom of the page. Modifying the threshold value can help removing 'noise' from the display. A greyscale operates above the threshold, with regions of higher similarity showing as darker diagonals. The numbers on this scale are arbitrary values in a range from 0 to 255.
Ensembl exons from 'known' and 'novel' transcripts are annotated as red or black boxes along each axis, respectively. Yellow rows and columns indicate their positions in the dot matrix display. Pointing at an exon shows the corresponding Ensembl Gene ID and clicking onto it leads to the corresponding 'GeneView' page. Grey outlined boxes along each axis annotate repeats in the genome sequence.
The display can be further customized using check boxes to the right of the display:
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Several Zoom boxes allow for selection of genome sequence regions between 0.5 kb and 20 kb.
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A 'Grid' box toggles the display of grid lines on the dot plot.
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A 'HSPs' box leads to a display of alignments of high-scoring segment pairs in the region. Please note that only HSPs exceeding the current threshold score are displayed.
The species, as well as the chromosome coordinates of both regions aligned are shown above and to the left of the display. Clicking the coordinates will lead to the same sequence region displayed in 'ContigView'.
References
1.
Erik L.L. Sonnhammer and
Richard Durbin
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
Gene. 1995 Dec 29; 167(1-2):GC1-10.
NCBI PubMed PMID:
8566757
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