DePiCt 2.0:
Degenerate Primer Design via Clustering
XINTAO WEI, GIRI NARASIMHAN
School of Computer
Science, Florida International University, University Park, Miami, FL 33199,
USA.
Software Release
Web
Version (Beta Version 2.0)
(
http://www.cs.fiu.edu/~giri/bioinf/DePiCt1.0/WebVersion/2depict.htm) (Release Oct 1, 2005)
Older Version (Version 1.0) (http://www.cs.fiu.edu/~giri/bioinf/DePiCt1.0/WebVersion/depict.htm)
[Work by Chris Archer and Jordan Farrow, December 2003].
Abstract
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
./DePiCt.pl
[-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:
./DePiCt.pl –h
show
the help information
./DePiCt.pl 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.
./DePiCt.pl –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]. )
Paper
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