PAMPS.EXE is the executable file for PAMPS algorithm, introduced by Najafabadi et al. (2008). PAMPS is an algorithm for solving Multiple Degenerate Primer Design (MDPD) problems.

How to use PAMPS.EXE:

PAMPS.EXE gets its parameters from command line using the following format:

PAMPS.EXE [input_file] [l_min] [d_max] [output_file]

input_file: The path of the FASTA file including input sequences
l_min: minimum length of the primers to be generated
d_max: maximum degeneracy of the primers to be generated
output_file: The path of the file in which the data of the generated primers are to be written

output_file has the following format:

>primer_name
...............................................sequence..............................................
....position of split points (1 indicates a split point just before the corresponding nucleotide)....

At the end of the output_file the running time in milliseconds is written.



*******************PAMPS-rsc.exe************************
This version of PAMPS is designed to use resources reliably with the minimum chance of unexpected program failure. It is generally slower than PAMPS.exe, yet it can be used for large input files with consistency. The I/O format of PAMPS-rsc.exe is the same as PAMPS.exe.



REFERENCES:

Najafabadi HS, Torabi N, Chamankhah M: Designing multiple degenerate primers via consecutive pairwise alignments. BMC Bioinformatics.