STACK_PACK EST CLUSTERING MANAGEMENT AND ANALYSIS TOOL-SUITE AVAILABLE

Win Hide winhide at sanbi.ac.za
Thu Sep 30 21:35:11 EST 1999


STACK_PACK EST CLUSTERING MANAGEMENT AND ANALYSIS TOOL-SUITE now
available

SANBI announces the free academic availability of the STACK_PACK EST
clustering management and analysis tool-suite.

STACK_PACK 1.0 has been developed by SANBI in collaboration with
Electric
Genetics, Cape Town (PTY) LTD, to support analysis of the increasing EST
load for Gene Discovery.

The tool-suite interchangeably supports 'modules' such as PHRAP and
other assemblers, and includes D2-cluster and CRAW together with other
codes specifically developed for the system.

STACK_PACK manages flow and stringent analysis of data between these
applications. The system creates two outputs: a standard data set as
well as a more highly-qualified data subset based upon consensus
quality.

Alternate splicing and low quality EST consensi are also detected and
processed.

This system has been used to manufacture STACK, the sequence tag
alignment and consensus knowledgebase which is also distributed by
SANBI.
                       http://www.sanbi.ac.za/Dbases.html

Further information on the STACK-PACK system, and the clustering code
d2-cluster,is to be published in the Genome Research November issue.

'D2_cluster: A Validated Method for Clustering EST and Full-length cDNA
Sequences' John Burke, Dan Davison, and Winston Hide. Genome Research
November 1999.

and

'A comprehensive approach to clustering of expressed human gene
sequence: The Sequence Tag Alignment and Consensus Knowledgebase. R. T.
Miller, A. G. Christoffels, J. Burke,A. A. Ptitsyn, T. R. Broveak,
W. A. Hide. Genome Research November 1999.


Academics may download the STACK database and STACK-PACK codes from

www.sanbi.ac.za/CODES







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