Proposal: new menu layout, with examples

Gary Williams, Tel 01223 494522 gwilliam at
Tue May 1 14:47:57 UTC 2001

James and I have been discussing the program group structure.
We seem to have come to some sort of agreement on the following.

Some things like 'Feature tables' are place-holders for groups of
programs that probably ought to be written.

I'm sure there will be useful comments on the following:
(Are 'Profiles' and 'Patterns' similar enough to be merged?)

+       Consensus       (merging sequences to make a consensus)
+       Differences       
+       Dot plots         
+       Global alignment
+       Local alignment
+       Multiple alignment
+Display                (information + publication display, not just
stuff that plots results)
+Edit                   (sequence and annotation manipulation)
+Enzyme Kinetics        (just 'findkm' at present)
+Feature tables         (manipulation and display of feature tables)
+Help                   (help for the user, e.g. wossname, showdb,
+       2D Structure    (RNA structure)
+       Codon usage
+       Composition     (properties over the whole sequence, GFF not
+       CPG islands
+       Gene finding    (genes and other genomic features)
+       Patterns        (search for defined patterns) 
+       Primers
+       Profiles        (search for defined profiles) 
+       Repeats
+       Restriction enzymes
+       Transcribe      (transcription factors)
+       Translate
+       Mutate
+Phylogeny              (mainly the Phylip package)
+       2D Structure    (2D structure and topological features)
+       3D Structure
+       Composition     (properties over the whole sequence, GFF not
+       Patterns        (search for defined patterns) 
+       Mutate
+       Profiles        (search for defined profiles) 
+       Database indexing
+       Database creation 
+       Misc

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at  
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

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