polydot

Function

Description

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

The two sequences are placed on the axes of a rectangular image and (subject to threshold conditions) wherever there is a similarity between the sequences a dot is placed on the image.

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

polydot compares all sequences in a set of sequences, draws a dotplot for each pair of sequences by marking where words (tuples) of a specified length have an exact match in both sequences and optionally reports all identical matches to feature files.

Usage

Command line arguments


Input file format

polydot reads in a set of nucleic or protein sequences.

The sequences may or may not be aligned.

Output file format

A graphical image is displayed on the specified graphics device.

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

0 if successful.

Known bugs

None.

Author(s)

History

Target users

Comments