From owner-bionews@hgmp.mrc.ac.uk Wed Apr 4 17:29:12 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9353517B0E for ; Wed, 4 Apr 2001 17:29:08 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2E0C317AB4 for ; Wed, 4 Apr 2001 17:29:06 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6022) id EF68217C0D; Wed, 4 Apr 2001 17:29:02 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5E68117C01 for ; Wed, 4 Apr 2001 11:36:50 +0100 (BST) Received: from hades.is.co.za (hades.is.co.za [196.4.160.43]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4E0EA17ADF for ; Wed, 4 Apr 2001 11:36:43 +0100 (BST) Received: (from news@localhost) by hades.is.co.za (8.9.3/8.9.3) id MAA26511; Wed, 4 Apr 2001 12:36:30 +0200 (SAST) (envelope-from news) To: bionet-announce@net.bio.net Message-ID: <3ACAF9DC.B3BFA066@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: Major Revamp of stackPACK Transcript Reconstruction System Released (Academic) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: hades.is.co.za 986380590 225 196.38.142.108 Date: Wed, 4 Apr 2001 17:29:02 +0100 (BST) Sender: owner-bionews@hgmp.mrc.ac.uk Precedence: bulk Free Academic Availability of the stackPACK v2.1 Transcript Reconstruction and Variation Analysis Tools The South African National Bioinformatics Institute, in collaboration with Electric Genetics (South Africa), is happy to announce the academic availability of the **significantly enhanced** stackPACK v2.1 clustering toolset. The new system has been tested so far on datasets of up to 450 000 sequences at SANBI. StackPACK v2.1 is now available for Linux, SGI, Irix, Sun Solaris and Compaq for both Academic and Commercial users. The primary goal of stackPACK v2.1 is to significantly improve the ability to handle large data sets and large clusters. Academic users may now download stackPACK v2.1 from http://www.sanbi.ac.za/CODES/STACKPACK_REQUEST/ StackPACK is the most widely used transcript reconstruction and variation analysis system available and is employed by over a hundred key research sites worldwide. The stackPACK system processes EST and mRNA data through a pipeline consisting of a series of steps including optional masking, loose clustering, assembly and alignment, alignment analysis for variation (alternate splicing) in clusters/transcripts and linking of non-overlapping clusters by clone ID. The system is unique due to its visualization tools and efficient data management, using a relational database. StackPACK can be run either through command line or through an rapid web-based interface. - What's New - **The primary goal of stackPACK v2.1 is to significantly improve the ability to handle large data sets and large clusters.** · Single-cluster functions are now 'distributed' so the user may run simultaneous multiple assemble or masking jobs, even on a single cpu system. · the d2_cluster sequence clustering algorithm is 10 times faster and has reduced memory requirements. · User interface speed is significantly increased. · Both web-based and command line data extraction reports are faster and have and reduced memory requirements. **New viewing and reporting functions highlight potential areas of interest** - Export options now enable smoother data exchange with third-party programs, reducing the time spent reformatting or parsing output. · Four new display options allow rapid assessment of the assembly and assembly analysis alignment views. · Alignments may be output directly to MSF and CLUSTAL formats. · Two additional data extraction reports, listing all constituent EST or mRNA sequences of all clusters and outputting the Alignment Analysis CRAW logs for all clusters. **Enhancements in terms of user flexibility and control of the pipeline processes and applications** · Undo option for most of the steps in the pipeline, allowing the reversal of all steps subsequent to and including the step being undone. · Ability to mask sequences using either cross_match or RepeatMasker, or to cluster unmasked or externally masked data. · Configuration file expansion allows significantly enhanced parameter flexibility. - Many new parameters are added to the configuration file including the number of cpus for multi-processor steps, additional program flags and specific program locations. ----- stackPack can be provided on a server to your community, contact liza@egenetics.com for information on server setup. ----- Interested in transcript reconstruction? STACKers mail 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 peer-reviewed 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 - StackPACK, originally developed at the South African National Bioinformatics Institute, is further developed and maintained by Electric Genetics who also provides free support for academic users. For queries about stackPACK v2.1 or assistance with download and installation, email: support@egenetics.com For further information on stackPACK, refer to the Electric Genetics website at: http://www.egenetics.com/?Section=Stackpack&Parent=products For further information on research at the South African National Bioinformatics Institute, please visit: http://www.sanbi.ac.za/Research.html ------------------------------------------------------------------------------------------------ .