Script for creating a dotplot
Requires matplotlib, numpy, biopython, pandas and tqdm. It scores the sequences with blosum62 matrix and shows the dotplot above some threshold. Unfortunately, it is not the fastest script and for long sequences (~2000 aa) it takes even 30 min with window size of 20 aa. Small sequences work quite well (1 - 10 s) dependingon the word size.
UPDATE1:
- update of the script so now it runs ~100 faster or even more for longer sequences
How to use the script:
sequence_dotplot.py -f fasta.file -s1 1 -s2 0 -w 10 -t 50
-f fasta file format with sequences -s1 / -s2 sequence number in the file (if the same sequence use the same number) -w windo size of calulated aligement -t treshold of measured values in % of 100 corresponding aminoacids in sequence
