STACK GENE INDEX 2.31 + CLUSTERING and MANAGEMENT TOOLS RELEASED

Win Hide winhide at sanbi.ac.za
Mon Dec 6 10:52:19 EST 1999


SANBI announces the release of  STACK - 2.31 : A Whole aligned Gene
Index of Human sequences, as well as underlying tissue specific indices.
The release is regularly updated with cross-links to UniGene and is
supported with consensus, assembly analysis and alignment viewing and
extraction at SANBI's website www.sanbi.ac.za/Dbases.html. The database
is the only currently existing system that includes a co-distribution of
the tools used to cluster and manage the production of the data.

STACK_PACK 0.8 alpha: Serial-capable, Parallelised versions of the
clustering code(s) are currently available for SGI, SUN and LINUX
platforms, (COMPAQ to be released very shortly).

STACKdb 2.31 is the first STACKdb release that contains the
whole-body-index section derived from the tissue-based clusters of the
same release.  In the past, the whole-body index section was delivered
after the tissue-based clusters.

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

The distribution contains documentation such as:

  * HOWTO.txt             how to get the most from searching STACKdb
  * STACK2.31_notes.txt   release notes and statistics for tissue-based
clusters
  * index2_31.txt         release notes and statistics for
whole-body-index
  * tissue_tree.txt       strategy for separating ESTs into tissue
categories














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