DOTPATHP

Displays a non-overlapping wordmatch dotplot of two sequences

A dotplot is a graphical representation of the regions of similaritybetween two sequences.

The two sequences are placed on the axes of a rectangular image andwherever there is a similarity between the sequences a dot is placed onthe image.

Where the two sequences have substantial regions of similarity, manydots align to form diagonal lines. It is therefore possible to see at aglance where there are local regions of similarity.

dotpath is very similar to the program dottup which looksfor places where words (tuples) of a specified length have an exactmatch in both sequences and draws a diagonal line over the position ofthese words.

Using a longer word size thus displays less random noise, runsextremely quickly, but is less sensitive.

dotpath finds all matches of size -wordsize or greaterbetween two sequences. It then reduces the matches found to the minimalset of long matches that do not overlap. This is a way of finding the(nearly) optimal path aligning two sequences. It is not the trueoptimal path as produced by the algorithms used in water orneedle, but for very closely related sequences it will producethe same result and will work well with very long sequences.

If you wish to compare the path found by dotpath to the set ofall matches found then the qualifier -overlaps will show allmatches in red except for the matches in the minimal path which areshown in black, as normal.