NormFinder 0.953 – Normalization of Real-Time Quantitative Reverse Transcription-PCR Data

NormFinder 0.953

:: DESCRIPTION

NormFinder is an algorithm for identifying the optimal normalization gene among a set of candidates.It ranks the set of candidate normalization genes according to their expression stability in a given sample set and given experimental design.NormFinder can analyze expression data obtained through any quantitative method e.g. real time RT-PCR and microarray based expression analysis.

::DEVELOPER

Department of Molecular Medicine, Aarhus University Hospital

:: SCREENSHOTS

:: REQUIREMENTS

Excel / R package

:: DOWNLOAD

NormFinder

:: MORE INFORMATION

Citation

C.L., Ledet-Jensen J., Ørntoft T.
Normalization of real-time quantitative RT-PCR data: a model based variance estimation approach to identify genes suited for normalization – applied to bladder- and colon-cancer data-sets.
Cancer Research. 2004 (64): 5245-5250

MAIRA 0.1.7 – Real-time Taxonomic and Functional analysis of long Reads on a laptop

MAIRA 0.1.7

:: DESCRIPTION

MAIRA is a new standalone program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop without internet access. The program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph.

::DEVELOPER

the Algorithms in Bioinformatics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

MAIRA

:: MORE INFORMATION

Citation

Albrecht B, Bağcı C, Huson DH.
MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.
BMC Bioinformatics. 2020 Sep 17;21(Suppl 13):390. doi: 10.1186/s12859-020-03684-2. PMID: 32938391; PMCID: PMC7495841.

Q-Gene 1.2 – Process Quantitative Real-time RT-PCR Data

Q-Gene 1.2

:: DESCRIPTION

Q-Gene is an application for the processing of quantitative real-time RT–PCR data. It offers the user the possibility to freely choose between two principally different procedures to calculate normalized gene expressions as either means of Normalized Expressions or Mean Normalized Expressions. In this contribution it will be shown that the calculation of Mean Normalized Expressions has to be used for processing simplex PCR data, while multiplex PCR data should preferably be processed by calculating Normalized Expressions. The two procedures, which are currently in widespread use and regarded as more or less equivalent alternatives, should therefore specifically be applied according to the quantification procedure used.

::DEVELOPER

Perikles Simon

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Microsoft Excel

:: DOWNLOAD

Q-Gene

:: MORE INFORMATION

Citation

Simon P.
Q-Gene: processing quantitative real-time RT-PCR data.
Bioinformatics. 2003 Jul 22;19(11):1439-40.