Free academic availability of stackPACK clustering tools for SGI Irix.

Liza Groenewald liza at egenetics.com
Fri Oct 6 04:46:52 EST 2000


We are happy to announce the availability of stackPACK v2.0 for SGI Irix
6.5.
Academic users are now able to download stackPACK v2.0 for Irix, in
addition to
Linux, with Sun and Compaq to follow soon, from the following address:

http://www.sanbi.ac.za/CODES/STACKPACK_REQUEST/

The stackPACK system processes EST and mRNA data through a pipeline
consisting
of a series of steps including masking, loose clustering, assembly and
alignment, alignment analysis for variation in clusters/transcripts and
linking non-overlapping clusters by clone ID. The system is unique not
only because of its scientific schema but also because of its efficient
management of the clustering data, using a relational database – the
program can be accessed through an effective web-based interface and
viewing tools or through command line.


The method employed and assessment of quality of the resource is fully
described in:
A Comprehensive Approach to Clustering of Expressed Human Gene Sequence:
The Sequence Tag Alignment and Consensus Knowledge Base
Robert T. Miller, Alan G. Christoffels, Chella Gopalakrishnan, John
Burke, Andrey A. Ptitsyn, Tania R. Broveak, and Winston A. Hide.
November 1999: Genome Research: 9:1143-1155

And

d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA
Sequences.
John Burke, Dan Davison, and Winston Hide.
November 1999: Genome Research: 9:1135-1142

Please also refer to the Electric Genetics website at
http://www.egenetics.com/?Section=Stackpack&Parent=products
for further information on stackPACK .


--
Liza Groenewald
Product Manager

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