| What is Staden?
Staden is a package of programs designed for sequence handling
and analysis. It is particularly useful for analysis of sequence
trace data and large scale sequence assembly projects.
What are the main programs in the staden
package? gap 4
Performs assembly, contig joining, assembly checking, repeat
searching, experiment suggestion, read pair analysis and contig
editing. Has graphical views of contigs, templates, readings
and traces which all scroll in register. Contig editor searches
and experiment suggestion routines use phred confidence values
to calculate the confidence of the consensus sequence and hence
only identify places requiring visual trace inspection or extra
data. The result is extremely rapid finishing and a consensus
of known accuracy.
pregap4
Provides a graphical user interface to set up the processing
required to prepare trace data for assembly or analysis; and
also gives a method for its automation. The possible processes
which can be set up include trace
How do I access staden?
Staden is installed on the genetics.wayne.edu server. You
can connect to this server with telnet and start an X-Windows
or VNC session. The binaries are located in /usr/local/staden-solaris-2001.0/solaris-bin
Where can I find help about staden?
The staden manual is located at here.
If you need help to access and use staden, contact danliu@genetics.wayne.edu
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