Tag: Design Primer

GenoFrag 2.1 – Design Primers Optimized for Whole Genome Scanning by Long-range PCR Amplification

GenoFrag 2.1

:: DESCRIPTION

GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in ～10 kb‐long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.

::DEVELOPER

GenoFrag Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/Unix/MacOsX
  • Python

:: DOWNLOAD

 GenoFrag Source Code

:: MORE INFORMATION

Citation

Nouri Ben Zakour et. al.
GenoFrag: software to design primers optimized for whole genome scanning by long‐range PCR amplification
Nucl. Acids Res. (2004) 32 (1): 17-24

PhiSiGns 1.2 – Indentify Signature Genes in Phages and Design Primers

PhiSiGns 1.2

:: DESCRIPTION

PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples. PhiSiGns is intended for phage biologists who want to find common conserved genes in phages for evolution or phylogeny based studies, or who are interested in designing primers that can be used to explore environmental phage diversity.

PhiSiGns Online Version

::DEVELOPER

the Breitbart lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhiSiGns

:: MORE INFORMATION

Citation:

Bhakti Dwivedi, Robert Schmieder, Dawn B. Goldsmith, Robert A. Edwards, and Mya Breitbart (in review)
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.
BMC Bioinformatics 2012, 13:37

QDD 3.1.2 / QDD-VM 3.1.2 – Select Microsatellite Markers and Design Primers

QDD 3.1.2 / QDD-VM 3.1.2

:: DESCRIPTION

QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input.

QDD-VM (QDD in a virtual machine) is an easy but greedy installation. The virtual machine (VM) comes with QDD and (almost) all its dependencies installed in a Galaxy server.

::DEVELOPER

Emese Meglécz and Jean-François Martin

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 QDD / QDD-VM

:: MORE INFORMATION

Citation

Meglécz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N., Martin, J.F. 2010.
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.
Bioinformatics 2010; Vol. 26,3 : 403-404; doi: 10.1093/bioinformatics/btp670.

Expeditor 2 – Design Primers using Human Gene Structure and EST information of your Species

Expeditor 2

:: DESCRIPTION

Expeditor is a tool for designing gene-specific primers targeted at genomic regions of interests based on known gene structure and EST sequence information

::DEVELOPER

NAGRP Bioinformatics Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

J Hered. 2005 Jan-Feb;96(1):80-2. Epub 2004 Dec 14.
Expeditor: a pipeline for designing primers using human gene structure and livestock animal EST information.
Hu ZL, Glenn K, Ramos AM, Otieno CJ, Reecy JM, Rothschild MF.