[EMBOSS] A note about fastA format(s) - Checked by AntiVir DEMO version -

[pmr at ebi.ac.uk]

Dear Guy,

> We are using EMBOSS version 3.0. One of my colleagues tried to use a
> multiple sequence file in fastA format, where each comment line starts
> with a string containing multiple pipe signs. An USA of type
> fasta::file:xx|yy|zz|uu|ss
> did not work. After some trial I found that putting "pearson" instead of
> "fasta" helped. This is strange, since according to the on-line manual at
> http://emboss.sourceforge.net/docs/themes/SequenceFormats.html
> "fasta" and "pearson" are synonyms. Here it seems that "fasta" is instead
> treated the same as "ncbi". Comments ?

Yes, that is indeed true. We had to make chanhes to support various NCBI
formats, and made FASTA and NCBI the same. We kept "pearson" as the
original plain fasta format.

We will update the documentation - it will take a little time to check for
any other changes to the formats.

regards,

Peter