Some future ideas about formats

[Guy Bottu]

>	Eventually people are going to get the idea that EMBOSS should be
>able to do things with data other than just sequences and want to run
>e.g. microarray and structure type analyses. With the current database
>definitions in emboss.default there is a type: clause that is not
>required. I would propose to make this mandatory and extend the values. 
>
>N is nucleotide sequence database
>P is protein sequence database
>S is a structure database
>M is a microarray experiment database.
>
>The USA can then be extended to cover structures (pdb:1HTF) for an example
>and microarray experiments. There are probably other entities that could
>be included.
>

The way EMBOSS handles sequences is certainly a vast improvement over GCG and 
should be extended to other kinds of data. But why limit ourselves to structures 
and microarray data ? There are other kinds of data that are handled by many 
software packages and that hence hange around in several alternative formats :
amino acid symbol comparison tables, codon usage tables, sequence motifs defined 
as patterns/profiles/HMM's, phylogenetic trees, etc. It would be nice if they 
could all be imported in a transparent way and exported in a user-chosen format 
directly from the program that creates it. 

	Guy Bottu,
	Belgian EMBnet Node