From owner-bionews@hgmp.mrc.ac.uk Thu Sep 6 18:20:51 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8268517C99 for ; Thu, 6 Sep 2001 18:20:48 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5B3C417C9F for ; Thu, 6 Sep 2001 18:20:36 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6022) id B484817C99; Thu, 6 Sep 2001 18:20:19 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0438917C97 for ; Thu, 6 Sep 2001 11:21:35 +0100 (BST) Received: from helios.is.co.za (helios.is.co.za [196.4.160.81]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D6ECB17C69 for ; Thu, 6 Sep 2001 11:18:54 +0100 (BST) Received: (from news@localhost) by helios.is.co.za (8.9.3/8.9.3) id MAA36742; Thu, 6 Sep 2001 12:18:39 +0200 (SAST) (envelope-from news) To: bionet-announce@net.bio.net Message-ID: <3B974F61.A76DBDC7@egenetics.com> From: Liza Groenewald X-Mailer: Mozilla 4.74 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.announce Subject: New release of STACKdb, in relational database format. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: helios.is.co.za 999771518 235 196.38.142.108 Date: Thu, 6 Sep 2001 18:20:19 +0100 (BST) Sender: owner-bionews@hgmp.mrc.ac.uk Precedence: bulk Major revamp of the STACKdb Human Gene Expression Index, provided free to academics, incorporates mRNA sequences and visualization software. ------------------------------------ The latest version of the STACK database of reconstructed human expressed transcripts, STACKdb v3.0, has been released by The South African National Bioinformatics Institute (SANBI), in collaboration with Electric Genetics. The STACK human gene expression index is unique in that it is the only gene expression index that is availabe with the tools that are used in its manufacture. In addition, it contains verified, clone-linked cluster assemblies. The index is processed into hierarchically organized human transcript consensus sequences that reflect gene expression forms and, in particular, alternate expression variants, within several tissue-based and one disease expression category. STACKdb v3.0 is created from 2,524,209 EST sequences and 51,638 partially redundant mRNA sequences, distributed according to tissue expression, and represents an increase of 569,014 new EST sequences and 51,638 mRNA sequences as compared to the previous release, STACKdb v2.4. STACKdb v3.0 contains 241,258 clusters and 12,943 clonelinks in total. What's New --------------------------------------- STACKdb 3.0 has been produced with the latest generation stackPACK transcript reconstruction and variation analysis management tools, and therefore has several fundamental improvements: * Inclusion of mRNA sequences in clusters. * The database is now distributed in two forms: - Relational database tables, for use with the web-based viewing software. - FastA files containing non-redundant sets of linked clusters, clusters and singletons for each tissue type, for use with external programs. * Web-based viewing software, equivalent to that found in stackPACK v2.1.1, which: - highlights variation. - allows the viewing of cluster, linked cluster and alternate consensus sequences. - displays initial (PHRAP) alignments, alignment analyses (CRAW output), as well as alignments for each potential alternate expression form. * Various web-based and command line reports to extract data for use in other programs. Availability ------------------------------- The database is available free of charge to academic and non-profit institutions. Interested users who wish to download STACKdb 3.0 may register at www.sanbi.ac.za/CODES. The Swiss Institute of Bioinformatics collaborates with SANBI and serves SANBI's STACKdb download from the Swiss Institute of Bioinformatics web site to ensure faster download times. The database may also be searched on-line by comparing a query sequence to any of the STACKdb categories. WebBLAST is available at: http://juju.egenetics.com/stackpack/webblast.html The stackPACK tools, used to create STACKdb, are also available free of charge to academics. Interested users may register at www.sanbi.ac.za/CODES to download the stackPACK tools for COMPAQ, Linux, Silicon Graphics or Sun platforms. Interested in transcript reconstruction? ----------------------------------------------- The STACKers mailing list is for information on EST clustering and transcript reconstruction. Please point your browser to the following URL in order to subscribe to STACKers: http://fling.sanbi.ac.za/mailman/listinfo/stackers Scientific Publications ------------------------------------------- StackPACK has been described in several publications. * The method employed and assessment of quality of the resource is fully described in: STACK: sequence tag alignment and consensus knowledgebase. Christoffels A, Gelder Av, Greyling G, Miller R, Hide T, Hide W. Nucleic Acids Res. 2001 Jan 1;29(1):234-8. and 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 * The clustering algorithm employed in stackPACK is described in: 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 Additionally, stackPACK has been instrumental in several discoveries. A listing of scientific publications and posters involving stackPACK can be found at: http://www.egenetics.com/?Section=publications&Parent=science Contact Details ---------------------------- STACKdb is managed and distributed by Electric Genetics who also provides free support for academic users. Please contact support@egenetics.com for support, feedback or any queries. For further information on STACKdb, please refer to the Electric Genetics website: http://www.egenetics.com/?Section=STACKdb&Parent=products For further information on research at the South African National Bioinformatics Institute, please visit: http://www.sanbi.ac.za/Research.html .