DePiCt 2.0: Degenerate Primer Design via Clustering



School of Computer Science, Florida International University, University Park, Miami, FL 33199, USA. 


Software Release

Web Version (Beta Version 2.0) ( (Release Oct 1, 2005)
Older Version (Version 1.0) (
[Work by Chris Archer and Jordan Farrow, December 2003].



Degenerate primers are useful for designing degenerate primers for homologous genes/proteins. However, when a large collection of sequences is considered, no consensus region may exist in the multiple alignment, making it impossible to design a single pair of primers for the collection. In such cases, manual methods are resorted to find smaller groups from the input collection so that primers can be designed for individual groups. This software package implements a new strategy for designing degenerate primers for a given multiple alignment of amino acid sequences. Our strategy proposes an automatic grouping of the input sequences from the multiple alignment by using clustering techniques. The groups are then dealt with individually. Conserved regions are detected for each group. Degenerate primers are then designed by reverse translating the conserved amino acid sequences to the corresponding nucleotide sequences. DePiCt 1.0, was written in BioPerl and was tested on the Toll-Interleukin Receptor family of plant resistance genes.


Input command line and their output

./ [-h] [-p prot_align_format] [-s MinPrimerLength] [-l MaxPrimerLength] [-n MinPrimerLength] [-m MaxPrimerLength] [-G default_genetic_code] [-g genetic_code_file] AlignedSequencesFile ResultFile

For example in the Linux environment, you can run this software by typing:

./ h 

    show the help information

./ AlignedSequences.msf   ResultFile

(AlignedSequences.msf is the input protein alignment file name; ResultFile is the output file.)

A sample output is shown in TIRResults.doc.

./ s 20 l 28   AlignedSequences.msf  ResultFile

(AlignedSequences.msf is the input protein alignment file name; ResultFile is the output file.

                          The minimum primer length can be provided with the -s option [default is 18].

                          The maximum primer length can be provided with the -l option [default is 27]. )



X. Wei, D. Kuhn, G. Narasimhan, Degenerate primer design via clustering, Proceedings of the IEEE Computer Society Bioinformatics Conference, pp 75-83, Stanford, CA, August 2003. [Pdf version]


Last Changed

October 1, 2005