Protein Sequence Dot Plot Analyzer

Sequence 1 (FASTA format):

Sequence 2 (FASTA format):

Or load sequences from file:

Select FASTA files (supports multiple sequences)

Window Size:

Similarity Threshold (%):

Scoring Method:

Color Scheme:

Dot Size:

Canvas Size:

Comparison Mode:

Pairwise Comparison All vs All Matrix

Instructions: The dot plot shows similarity between sequences with origin at bottom-left corner (0,0). Each dot represents a region where sequences match above the threshold. Choose between exact identity or evolutionary scoring matrices (BLOSUM62/PAM250) for more biologically relevant comparisons. Select color schemes including greyscale, heat maps, and rainbow for better visualization. Pairwise comparisons also show a similarity profile graph that tracks similarity along the sequence length. Export options become available after generating plots.

Protein Sequence Dot Plot Analyzer

Sequence Similarity Profile