[Bioperl-l] EMBOSS/water interface

Mike Muratet muratem at eng.uah.edu
Thu Feb 3 11:53:17 EST 2005


I'm trying to implement the Bio::Factory::EMBOSS to the 'water'
method (which coincidentally is the one used in the man page example). I'm
using EMBOSS 2.9.0 which is the latest on the emboss website. I get an
error 'Died: Unknown qualifier -seqall' which I interpret to mean the
emboss water method complaining that -seqall is not a valid argument. It
is, however, used in the man page. Furthermore, I don't see any
documentation for Bio::Factory::EMBOSS in the module documentation at
bioperl.org. Is this an obsolete method? Has anyone ever got the example
in the manpage to work?



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