Future software directions

Keith Robison robison1 at husc10.harvard.edu
Thu Mar 25 14:45:24 EST 1993

mwd at cray.com (Mark Dalton) writes:

>        I want to see a free package available for researchers to do
>exactly what you asked for.  Basically the human genome project is supplying
>a lot of sequence (along with other projects) and the information is not
>really being looked at, even that which can be automated.

>These are my thoughts:

>This is the basic automated structure. It can be turned "on" or "off"
>at any point. It would be ideal to have both a text interface and
>GUI interface.  I would like to see the Graphic displays in X or motif.
>Also have output to postscript (black-white and color) printers or an
>option as ascii.

>      /RNA structure                    / Including known motifs
>     / comparison                      /
>    /                                 /structural
>   /RNA structure    /Motif search   / prediction
>  /                 /               /
>DNA sequence ------protein  ----- structure  --- structural similarity search
>   \                \
>    \Databank search \Databank search
>     \                \
>      \Multiple        \Multiple alignment
>       \sequence        \
>        \alignment       \
>         \              phylogenetic
>        phylogenetic    ananlysis
>        tree

<WARNING: shameless plug for a friend's work>

Sounds an awful lot like Steve Smith's GDE (okay, okay -- so you 
are "stuck using X-Windows").  -- available as always from
golgi.harvard.edu in the pub/GDE directory for the grand sum of $0.00.
Also, while some of your diagram isn't in GDE, GDE is fully user-extensible
so you are free to add whatever is missing.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at biosun.harvard.edu 

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