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MTG
MTG

Reputation: 301

Weblogo - selenocysteine alphabet

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

Answers (1)

MTG
MTG

Reputation: 301

My solution: Here what i've done

  1. Check if the infile do not have errors.

  2. add a alphabet 'ACDEFGHIKLMNPQRSTVUWY' to option -a

  3. 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

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