[EMBOSS] Antigenic - input file format?

[pmr at ebi.ac.uk]

Hi Sujata,

> I want to use the package called 'Antigenic' in EMBOSS.
> I am not quite clear about the input file format to be used.
>
> How can I input a fasta file to the program? - is it possible to use a
> text file that has the amino acid sequence in a fasta format? In which
> folder should the file be?

All EMBOSS programs read sequences from files, or from databases (local or
remote).

You can put the sequence in a file, in fasta format, and give the filename
to any EMBOSS program as input. Sequences are "input parameters" so simply
putting the filename on the command line is enough.

EMBOSS will look in the current directory, but you can give the full or
relative file path just like any Unix command.

This assumes of course that you are running EMBOSS locally, not through a
web interface (in that case, simply paste a FASTA format sequence into the
text box).

Hope that helps

Peter