## Threshold dotplot of two sequences

### Description

This tool uses Emboss program dotmatcher to generate a dotplot from two input sequences. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence using a specified substitution matrix. The two sequences are the axes of the rectangular dotplot. Wherever there is "similarity" between a position from each sequence a dot is plotted. The threshold conditions for "similarity" are defined by the user.

All positions from the first input sequence are compared with all positions from the second input sequence and scored, using the specified substitution matrix. This produces a matrix of scores from which local regions of similarity (corresponding to diagonals in the dotplot) are identified. A window of user-specified length is moved along all possible diagonals. Each position in the window corresponds to a pair-wise score from the scoring matrix. The score for the entire window is the sum of the scores for individual positions within it. If the window score is above the user-defined threshold, then a line is plotted on the dotplot corresponding to the window.

The input sequences can be in any of the EMBOSS compatible sequence formats.

For more details, please check the manual page of dotmatcher command.

### Output

Output is either an alignment report of sequence alignment file.