PerlPrimer 1.1.14 review

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PC

License: GPL (GNU General Public License) File size: 0K Developer: Owen Marshall

0

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. PerlPrimer aims to automate and simplify the process of primer design.

Here are some key features of "PerlPrimer":
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 or a local 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 Perl/Tk. In addition, for QPCR functionality PerlPrimer uses the open-source Spidey executable from NCBI, and restriction enzyme data from the REBASE project is used when adding cloning sites. 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.

What's New in This Release:
Ensembl compatibility restored once again (slight change in the searchview output was causing problems)