[Bioperl-l] Bio::Prospect:: -- a Perl interface to Prospect protein threading

Reece Hart rkh at gene.com
Wed Feb 18 16:31:05 EST 2004

bioperl-l gang:

We're pleased to announce the first public release of Bio::Prospect::, a
Perl API for protein fold recognition with Prospect PRO.  A
mini-manuscript describing the module is available at

        We present Bio::Prospect::, an object-oriented Perl Application
        Programming Interface (API) to the PROSPECT protein threading
        application. The Bio::Prospect:: modules facilitate executing
        the program, parsing the results, generating a homology model
        from an alignment, preparing a model for display with RasMol,
        and reconciling multiple pairwise alignments as a single
        multiple sequence alignment. The Bio::Prospect:: modules provide
        for local and remote execution of PROSPECT via a consistent
        interface. PROSPECT results may be represented with the
        full-featured Thread class or as a space-efficient distillation
        of results with the ThreadSummary class; instances of both
        classes may be serialized for network transmission of results
        from remote execution.

LICENSE: The module is released under the  Academic Free License v. 2.0

AVAILABILITY: The project is hosted on SourceForge
(http://www.sourceforge.net/projects/prospect-if/). A perl install
package is available through CPAN (http://search.cpan.org/~reece/).
Example scripts are included.

REQUIREMENTS: This module requires Prospect PRO
(http://www.bioinformaticssolutions.com/products/prospect.php) and
several other perl modules, all available from CPAN.

Comments, bug reports, patches, and code contributions are encouraged.

Happy Threading,
Reece Hart and David Cavanaugh

Reece Hart, Ph.D.                       rkh at gene.com, http://www.gene.com/
Genentech, Inc.                         650/225-6133 (voice), -5389 (fax)
Bioinformatics and Protein Engineering
1 DNA Way, MS-93                        http://www.in-machina.com/~reece/
South San Francisco, CA  94080-4990     reece at in-machina.com, GPG: 0x25EC91A0

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