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

chipPCR 1.0-2 – Toolkit of helper Functions to pre-process Amplification data

chipPCR 1.0-2

:: DESCRIPTION

The chipPCR package is a toolkit of functions to preprocess amplification curve data.

::DEVELOPER

Stefan Roediger [cre, aut], Michal Burdukiewicz [aut], Konstantin A. Blagodatskikh [ctb]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 chipPCR

:: MORE INFORMATION

Citation:

chipPCR: an R package to pre-process raw data of amplification curves.
Rödiger S, Burdukiewicz M, Schierack P.
Bioinformatics. 2015 Apr 24. pii: btv205.

Digital Karyotyping 1.0.1 – Detecting DNA Copy Amplifications

Digital Karyotyping 1.0.1

:: DESCRIPTION

Digital Karyotyping (DK) is a method that provides quantitative analysis of DNA copy number at high resolution. DK uses cleaving enzymes to obtain unique tags (short but representative DNA sequences) at approximately 4 kb intervals along the entire genome.

::DEVELOPER

Chao-Ling Chang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 Digital Karyotyping

:: MORE INFORMATION

Citation

Digital karyotyping: an update of its applications in cancer.
Salani R, Chang CL, Cope L, Wang TL.
Mol Diagn Ther. 2006;10(4):231-7.

PriSM – Primer Selection and Matching for Amplification of Viral Genomes

PriSM

:: DESCRIPTION

PriSM is a set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Yu Q, Ryan EM, Allen TM, Birren BW, Henn MR, Lennon NJ (2011)
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.
Bioinformatics 27(2): 266-267.

BASTA – Bayesian Modeling of DNA copy number amplification data

BASTA

:: DESCRIPTION

BASTA contains an implementation of a Bayesian model-based method for unsupervised classification of tissue samples based on DNA copy number amplifications.

::DEVELOPER

Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  BASTA

:: MORE INFORMATION

Citation:

Marttinen, Pekka, Myllykangas, Samuel and Corander, Jukka (2009)
Bayesian clustering and feature selection for cancer tissue samples
BMC Bioinformatics 2009, 10:90