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Find best diagonals

This option is the fastest and can be useful for a quick comparison of two long DNA sequences. The algorithm is as follows. First it finds the positions of runs of identical characters ("words") of length word length, as for the find matching words algorithm. Now imagine a diagonal line running from corner to corner of the diagram, at right angles to the diagonals created from Find matching words. The scores for the matching "words" are accumulated at the appropriate positions on this imaginary line, producing a histogram. The histogram is analysed to find its mean and standard deviation. The diagonals that lie above some cutoff score (defined in standard deviation units), are rescanned using the find similar spans algorithm. Any window lengths reaching the cutoff score produce a dot which is plotted in the usual way.


The dialogue box requests horizontal and vertical sequences and their ranges ( see section Selecting a sequence), the minimum number of identical characters in a run "word length", the minimum standard deviation, the window length and the minimum score.

The points are plotted to the sip plot ( see section Sip plot).

Further operations available for find best diagonals are:

This command gives a brief description of the sequences used in the comparison and the input parameters used.

horizontal EMBL: hsproperd
vertical EMBL: mmproper
window length 11 minimum score 9 word length 8 minimum sd 3.000000

A listing of all the matches is obtained in the output window. The horizontal (h) and vertical (v) positions of the beginning of the match are listed.

Positions       1066 h        905 v 
Positions       1067 h        906 v 
Positions       1068 h        907 v 
Positions       1069 h        908 v 
Positions       1070 h        909 v 
Positions       1071 h        910 v 
Positions       1072 h        911 v 
Positions       1073 h        912 v 
Positions       1074 h        913 v 

This option allows the line width and colour of the matches to be altered.See section Colour Selector. A colour browser is displayed from which the desired line width or colour can be configured. Pressing OK will update the sip plot.
Display sequences
Selecting this command invokes the sequence display ( see section Sequence display). Moving the cursor in the sequence display will move the cursors of the same sequence in any sip plot ( see section Cursors). To force the sequence display to show the nearest match, use the "nearest match" button in the sequence display plot.
This option removes the points from the sip plot but retains the information in memory.
This option will redisplay previously hidden points in the sip plot.
This command removes all the information regarding this particular invocation of Find best diagonals, and access to this data is lost.

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.