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Finding Matching Words

The find matching words routine finds runs of identical characters in the sequence. Its main value is speed, being hundreds of times faster than the find similar spans function. It is of course not very sensitive but is useful for long DNA sequences.


The dialogue allows the horizontal and vertical sequences and their ranges to be selected ( see section Selecting a sequence). The word length is the minimum number of consecutive matching characters. All runs of identical characters that are at least as long as the word length will produce a line on the SPIN Sequence Comparison Plot of length proportional to the actual word length ( see section SPIN Sequence Comparison Plot).

Further operations available for find matching words are:

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

horizontal EMBL: hsproperd
vertical EMBL: mmproper
word length 8 
Number of matches 140

A detailed listing of all the matching words is obtained in the Output Window. The horizontal (h) and vertical (v) positions of the beginning of the match are listed along with the length of the match and the match itself.

Positions        162 h          4 v and length         14
Positions        225 h         67 v and length         18
Positions        509 h        118 v and length          8
Positions        276 h        118 v and length          9
Positions        288 h        130 v and length          8
Positions        626 h        131 v and length          8
Positions       1208 h        144 v and length          8

Tabulate scores
This option lists scores, probabilities, and their expected and observed numbers of matches.

score    8 probability 2.06e-05 expected           43 observed 140
score    9 probability 5.35e-06 expected           11 observed 67
score   10 probability 1.39e-06 expected            3 observed 45
score   11 probability 3.60e-07 expected            1 observed 35
score   12 probability 9.35e-08 expected            0 observed 22
score   13 probability 2.43e-08 expected            0 observed 18
score   14 probability 6.30e-09 expected            0 observed 17
score   15 probability 1.63e-09 expected            0 observed 11
score   16 probability 4.24e-10 expected            0 observed 9
score   17 probability 1.10e-10 expected            0 observed 9
score   18 probability 2.86e-11 expected            0 observed 8
score   19 probability 7.42e-12 expected            0 observed 6
score   20 probability 1.93e-12 expected            0 observed 5
score   21 probability 5.00e-13 expected            0 observed 3
score   22 probability 1.30e-13 expected            0 observed 2
score   23 probability 3.37e-14 expected            0 observed 2
score   24 probability 8.74e-15 expected            0 observed 2

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 SPIN Sequence Comparison Plot.
Display sequences
Selecting this command invokes the sequence display ( see section Sequence Comparison Display). Moving the cursor in the sequence display will move the cursors of the same sequence in any SPIN Sequence Comparison 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 SPIN Sequence Comparison Plot but retains the information in memory.
This option will redisplay previously hidden points in the SPIN Sequence Comparison Plot.
This command removes all the information regarding this particular invocation of Find matching words, and access to this data is lost.

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This page is maintained by staden-package. Last generated on 22 October 2002.