Reputation: 301
I want to generate logo with selenocysteine, but when i choose option with reduced_protein_alphabet i get error 'Repetative alphabet'
weblogo -f sc.txt -D fasta -o sc_logo -F pdf -a reduced_protein_alphabet -s large -n 100 -c chemistry
Upvotes: 1
Views: 109
Reputation: 301
My solution: Here what i've done
Check if the infile do not have errors.
add a alphabet 'ACDEFGHIKLMNPQRSTVUWY' to option -a
color aminoacids in this alphabet -C
weblogo -f sc.txt -D fasta -o logo -F pdf -n 100 -A protein -a 'ACDEFGHIKLMNPQRSTVUWY' -s large -C yellow U selenocysteine -C red DE acidic -C black AVLIPWFM Hydrophobic -C blue KRH basic -C purple QN Neutral -C green GSTYC Polar
I didn't realese it is that simple. Maybe it will help someone!
Upvotes: 1