Major Revamp of stackPACK Transcript Reconstruction System Released (Academic)

Liza Groenewald liza at egenetics.com
Wed Apr 4 11:30:42 EST 2001


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 at 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 at 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

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