GDE, sequence alignment/analysis in X

Operator root at harvard.edu
Tue Feb 19 14:22:17 EST 1991


The Genetic Data Environment (GDE) is going into beta release this week.
The binary only release will run on Sun SPARCstations under X windows.  The
core editor/display is written in XView, and follows the OpenLOOK style
guide.

The system is a modular set of programs for multiple sequence alignment
and analysis.  The GDE uses an expandable user interface, and
an external function calling mechanism.  This allows the immediate addition
of existing analysis functions to the system with only minor modification.
Analysis functions written in any language can be added without the need
to add a graphical user interface to them.

Key features include:

Color highlighting of sequence data.
Ability to handle large data alignments (limited by virtual memory only)
Several levels of sequence  protection
Split-screen editing
Group functions.

Current external functions include:

Automated sequence alignment
Homology searching against the NCBI database (network blast)
Limited phylogenetic analysis
Functions to demonstrate color attributing

The system is being released to interested parties in order to demonstrate
it's expandability.  Later releases will include full source code, and
other analysis functions currently under developement.

Groups interested in receiving a copy of the beta release should send email to
smith at nucleus.harvard.edu.



Steven Smith
Director of Computation
Harvard Genome Lab.
smith at nucleus.harvard.edu




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