[Biojava-l] Re: CORBADEV: LSR news - new RFP about biomolecular entities

Matthew Pocock mrp@sanger.ac.uk
Tue, 19 Sep 2000 14:02:32 +0100


> I have just two suggestions for addition:
> - a type for representing floating point information on sequence positions,
>   such as hydrophobicity plots. I am not going to insist on this, because the
>   (nearly) obvious solution is to just use a IDL::float. Or was that double ...

This can be cleanly represented as an alignment containing a sequence (protein) and
hydrophobicity (floats). This would require either a special type within alignments
that has numbers, or a re-working of how sequences are represented so that an
individual symbol could be a float (the neater solution). This may be covered by the
BioSequence alphabet extensions. I don't know how the alignment object works in BSA
so I may be way of mark.