[EMBOSS] pepinfo and ambiguous amino-acids

Hamish McWilliam hpm at ebi.ac.uk
Mon Jan 6 16:52:30 UTC 2014

Hi folks,

When trying to use pepinfo on sequences containing peptide ambiguity
codes (e.g. BJXZ) the program gives an error. For example running
pepinfo on UniProtKB:Q9DY04 gives:

Error: At position 83 in seq, couldn't find key X

This is a reference to these amino acid codes not having corresponding
entries in the data files used by pepinfo:

- Eaa_properties.dat
- Eaa_hydropathy.dat

It would be good if this was handled more gracefully, either by
providing "average" values in the data files, or by handling these cases
with a warning and an appropriate "null" value.

FWIW the same issue comes when handling sequences with unusual amino
acids (i.e. 'O' and 'U'), although there should be actual figures for these.

Does anyone have already fixed data files that could be used instead?

All the best,

Mr Hamish McWilliam,
Web Production,
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SD
United Kingdom

URL: http://www.ebi.ac.uk/

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