SAPrimer - A Software for Primer Design
Description
SAPrimer is a software that implements a Simulated Annealing (SA) strategy for searching primer
pairs for a given DNA or protein sequence. Primers can be design to amplify the entire input sequence
or just a frame (of a specified size) of the sequence.
To use the software, the user does not need any knowledge about SA. For a given input sequence, which can be pasted from clipboard or privided by a file (in fasta or text plain format), the search
can be performed using default values for the parameters used to evaluate a primer, as for example, lenght,
CG content, melting temperature and 3' end composition and for the parameters that controls the
SA (T and decreasing factor). The user can, however, change all the default values to better
adjust the search according to the real condition in which the primer pair will be used.
Publication
The first version of the software was described in Montera, L. & Nicoletti M.C. The PCR primer design as a metaheuristic search process. ICAISC 2008, Lecture Notes in Artificial Intelligence, v. 5097, pp. 963-973, 2008. In this version, just DNA sequences was considered as a valid input sequence for which only a single primer pair to amplify the entire sequence is searched.
The second version was describe as the chapter A Customized Simulated Annealing Suitable for Primer Design in Polymerase Chain Reaction Processes in the book Simulated Annealing, Theory with Applications edited by: Rui Chibante, ISBN: 978-953-307-134-3, Publisher: Sciyo, Publishing date: August 2010.
With this version of the SAPrimer the user can use as input a DNA or protein sequence and find for primer pairs that amplify the entire sequence or just a frame of a specified size.
Download
- SAPrimer (second version). If your operating system is using "dot" as a decimal separator.
- SAPrimer (second version). If your operating system is using "comma" as a decimal separator.
- Additional library You may need them to execute SAPrimer. After downloading the file,
unzip it at the same directory you put SAPrimer.
(last update on December 2010)
Others
For a primer found by the SAPrimer software, the associated Tm corresponds to the average among a number of formulas
propoused in the literature. If the user desire to do a more detailed study about the Tm, one can refers to the
the webserver lotacated at http://www.facom.ufms.br/~tmcomparisons/index.htm.
Contact
For comments, questions and report bugs, please contact Luciana Montera (montera@facom.ufms.br)