Find matching words

The find matching words routine finds runs of identical characters in the sequence. Its main value is speed, being 100's of times faster than the find similar spans function. It is of course not very sensitive but is useful for long DNA sequences.

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 sip plot of length proportional to the actual word length ( see section Sip plot).

If the expected number of matches is greater than a maximum value (currently set by default to be 5000) ( see section Changing the maximum number of matches), a dialogue box will be invoked (see below). This dialogue box displays the expected number of matches and an approximation of the memory required to save these matches. The user is then given the option of plotting the results only (temporary result) ( see section Permanent and temporary results), or saving the results in memory. It is strongly advised that for large numbers of matches that the results are only plotted.

Further operations

Information

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

Results

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
ttcacccagtatga
Positions        225 h         67 v and length         18
gaagactgctgtctcaac
Positions        509 h        118 v and length          8
ctctgtca
Positions        276 h        118 v and length          9
ctctgtcag
Positions        288 h        130 v and length          8
tgcaggtc
Positions        626 h        131 v and length          8
gcaggtct
Positions       1208 h        144 v and length          8
atggtcag

Configure

This option allows the line width and colour of the matches to be alteredSee 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 ( Display --> see section Sequence display). By moving the mouse in the sip plot whilst holding the left mouse button down, the sequences around the crosshair position are displayed. To force the sequence display to show the nearest match, use the "nearest match" button in the sequence display plot.

Hide all

This option removes the points from the sip plot.

Reveal all

This option will redisplay previously hidden points in the sip plot.

Remove

This command removes all the information regarding this particular invocation of Find matching words, and access to this data is lost.