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

CovaRNA / CovStat 1.16.0 – Detecting Long-range Covariations in Nucleotide Alignments

CovaRNA / CovStat 1.16.0

:: DESCRIPTION

CovaRNA / CovStat is a novel index-based computational method to detect long-range covariation on a genomic scale, as well as for determining the statistical significance of observed covariation patterns in alignment pairs.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C / R

:: DOWNLOAD

CovaRNA / CovStat

:: MORE INFORMATION

Citation:

Bindewald E, Shapiro BA.
Computational detection of abundant long-range nucleotide covariation in Drosophila genomes.
RNA. 2013 Sep;19(9):1171-82. doi: 10.1261/rna.037630.112. Epub 2013 Jul 25. PMID: 23887147; PMCID: PMC3753924.