Proposal: new menu layout, with examples
Gary Williams, Tel 01223 494522
gwilliam at hgmp.mrc.ac.uk
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?)
+Compare
+ 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,
seealso)
+Nucleic
+ 2D Structure (RNA structure)
+ Codon usage
+ Composition (properties over the whole sequence, GFF not
produced)
+ 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)
+Protein
+ 2D Structure (2D structure and topological features)
+ 3D Structure
+ Composition (properties over the whole sequence, GFF not
produced)
+ Patterns (search for defined patterns)
+ Mutate
+ Profiles (search for defined profiles)
+Utils
+ Database indexing
+ Database creation
+ Misc
+Test
--
Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK
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