Application note: A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs

Long non-coding RNAs (lncRNAs) are of fundamental biological importance; however, their functional role is often unclear or loosely defined as experimental characterization is challenging and bioinformatic methods are limited. We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs within the genome. It combines annotation, normalization and gene expression with sequence-structure conservation, functional interactome and promoter analysis. Our protocol allows an analysis based on the tissue and biological context, and is powerful in functional characterization of experimental and clinical RNA-Seq datasets including existing lncRNAs. This is demonstrated on the uncharacterized lncRNA GATA6-AS1 in dilated cardiomyopathy.

You can find here the supplement information describing in detail the workflow combining gensearchNGS with other tools used in the work published here:

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs
Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Ke Xiao, Thomas Thum, David Atlan, Hans-Ulrich Prokosch, Thomas Dandekar
Briefings in Bioinformatics, Volume 21, Issue 4, July 2020, Pages 1391–1396, https://doi.org/10.1093/bib/bbz066
Published: 03 October 2019

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Application note: A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs

Long non-coding RNAs (lncRNAs) are of fundamental biological importance; however, their functional role is often unclear or loosely defined as experimental characterization is challenging and bioinformatic methods are limited. We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs within the genome. It combines annotation, normalization and gene expression with sequence-structure conservation, functional interactome and promoter analysis. Our protocol allows an analysis based on the tissue and biological context, and is powerful in functional characterization of experimental and clinical RNA-Seq datasets including existing lncRNAs. This is demonstrated on the uncharacterized lncRNA GATA6-AS1 in dilated cardiomyopathy.

You can find here the supplement information describing in detail the workflow combining gensearchNGS with other tools used in the work published here:

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs
Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Ke Xiao, Thomas Thum, David Atlan, Hans-Ulrich Prokosch, Thomas Dandekar
Briefings in Bioinformatics, Volume 21, Issue 4, July 2020, Pages 1391–1396, https://doi.org/10.1093/bib/bbz066
Published: 03 October 2019

Wuhan COVID19 flu

As the coronavirus disease hits pandemic proportions we have included the current ASM985889v3 RefSeq to help support the research community in the field as well as technical improvements to our software to ease user inclusion of updates of this RefSeq that will certainly be deposited in the NCBI databases. Phenosystems SA has also committed to provide free of charge one year licenses to any laboratory, private or public, wishing to analyse SARS-CoV2 or other related coronaviruses in this fight against COVID-19. We will also provide support to these labs as far as possible during these difficult times.

You can download the application note here.

Please contact us for further information and the free licences.

 

Oracle Java licensing

Oracle has decided to change its licensing model with the end of Java 8: Java support roadmap info here.

If you are using Gensearch, you are not impacted by this change, as the Software is compiled to native code by us, and thus includes the relevant Java run-time packages, you don't need to even have Java installed on your machine.

If you are using GensearchNGS you either have opted for a native compiled version for Windows OS, in this case you are also not impacted by this change. The native compiled version has two disadvantages: you can't update it by using the built-in update system, and the native version runs only on single CPU systems, not servers or high-end Desktops with dual-CPUs.

In case you are using GensearchNGS as a Java class package (jar file) on a locally installed Java run-time, Oracle offers a license free drop in replacement with OpenJDK:

Info about Oracle releases for Java 11 and later here.

This OpenJDK JRE is functionally identical to the now license fee covered Oracle JDK (minus a few 'Enterprise' functionalities that are not used by GensearchNGS and thus not relevant in our case).

You can download the free drop-in replacement, OpenJDK 11 LTS (long term support) at the following link:

Download links for Java 11 here.

It will also explain you the installation process.

Translation of the Genetic Variant Interpretation Tool (ACMG/AMP)

With permission from Linda Jeng, MD, PhD, FACMG, (University of Maryland), and collaboration with molecular diagnostics partners in France and Czech Republic, we are now offering translations in French and Czech of their "Genetic Variant Interpretation Tool". We are open to collaborate with diagnostics laboratories in other countries to translate it into further languages.

You can find the French version here.

You can find the Czech version here.

Gensearch moves to 4.4 and provides submission tool to Clinvar

Gensearch latest release is now available with the 4.4 version. Germany has implement new regulations concerning reimbursement of genetic diagnostic tests, these include now a financial compensation for publication of novel clinically relevant variants to publicly accessible databases. Phenosystems has developed a module to submit variants to Clinvar to facilitate the work process and allow German labs to be reimbursed for this aspect in a user-friendly efficient way. Of course this module can be used by all our customers with current active support contract. In a second phase we will deploy this module also to GensearchNGS

Please contact us for more information.

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