From owner-announce@net.bio.net Fri Oct 01 01:35:00 1999 Path: biosci!biosci!not-for-mail From: Win Hide Newsgroups: bionet.announce Subject: STACK_PACK EST CLUSTERING MANAGEMENT AND ANALYSIS TOOL-SUITE AVAILABLE Date: 30 Sep 1999 19:35:11 -0700 Organization: An Internet Solution Customer Lines: 50 Sender: daemon@net.bio.net Approved: kristoff@net.bio.net Distribution: world Message-ID: <7t16kv$ig6@net.bio.net> NNTP-Posting-Host: net.bio.net 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 .