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PerlPrimer v1.1.3 (cross-platform PCR software)

Owen Marshall owen.marshall at mcri.edu.au
Mon Apr 26 01:53:12 EST 2004


Version 1.1.3 of PerlPrimer is available at http://perlprimer.sourceforge.net.
This release adds several new features to QPCR primer design, including the
ability to design primers against a particular exon or range of exons, and the
ability to design primers that do not overlap an intron/exon boundary (less
specific, but useful with difficult to amplify genes).  PerlPrimer can now
receive data from other applications via TCP sockets (currently used by Python
Contig Viewer (http://www.atgc.org/Py_ContigViewer/)).  A Windows installer
containing the Win32 Spidey executable and a standalone executable version of
PerlPrimer is now available for Windows users (no need to install Perl or any
other software).

PerlPrimer is a free, open-source GUI application written in Perl that designs
primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.
It aims to automate and simplify the process of primer design.

PerlPrimer's current features include the following:

    * Calculation of possible primer-dimers
    * Retrieval of genomic or cdna sequences from Ensembl (including both
sequences automatically for QPCR)
    * Ability to BLAST search primers using the NCBI server
    * Results can be saved or optionally exported in a tab-delimited format
that is compatible with most spreadsheet applications.
    * ORF and CpG island detection algorithms
    * Ability to add cloning sequences to primers, automatically adjusted to be
in-frame
    * QPCR primer design without manual intron-exon boundary entry

PerlPrimer calculates primer melting temperature using J. SantaLucia's
extensive nearest-neighbour thermodynamic parameters. To adjust for the salt
conditions of the PCR, PerlPrimer uses the empirical formula derived by von
Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+,
dNTPs and primers, or use standard PCR conditions. The result is a highly
accurate prediction of primer melting temperature, giving rise to a maximum
yeild of product when amplified.

PerlPrimer is written in Perl and requires Perl/Tk. In addition, for QPCR
functionality PerlPrimer requires the open-source Spidey executable
(http://www.ncbi.nlm.nih.gov/spidey/) from NCBI. The program is designed to be
cross-platform compatible and has been developed and tested on both Microsoft
Windows and GNU/Linux-based operating systems. Users have also reported success
using the program under Mac OS X.

A tutorial giving some idea of PerlPrimer's capabilities is available at
http://perlprimer.sourceforge.net/tutorial.html

Feedback and suggestions welcome,

Owen Marshall
Chromosome Research
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road
Parkville Victoria 3052
Australia

T   +61 3 8341 6255
F   +61 3 9348 1391

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