XRNA 2.0 – Creation, Annotation & Display of RNA Secondary Structure Diagrams

XRNA 2.0

:: DESCRIPTION

XRNA is a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams.XRNA provides editing tools for easy modification of publication quality secondary diagrams that can be either drawn manually, or through automatic generation. Other features include grouping, numbering and structure annotation. XRNA secondary structures may be saved in a native format, or exported as postscript for printing and further manipulation in programs such as Adobe Illustrator.

::DEVELOPER

RNA Center, UCSC

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Perl

:: DOWNLOAD

XRNA

:: MORE INFORMATION

miRPara 6.3 – SVM-based miRNA Prediction tool

miRPara 6.3

:: DESCRIPTION

miRPara predicts most probable mature miRNA coding regions from genome scale sequences in a species specific manner. We classified sequences from miRBase into animal, plant and overall categories and used a support vector machine (SVM) to train three models based on an initial set of 77 parameters related to the physical properties of the pre-miRNA and its miRNAs. By applying parameter filtering we found a subset of ~25 parameters produced higher prediction ability compared to the full set.

::DEVELOPER

miRPara team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

miRPara

:: MORE INFORMATION

Citation:

Wu Y., Wei B., Liu H., Li T., Rayner S.
MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences.
BMC Bioinformatics. 2011 Apr 19; 12(1):107

VARUS 1.0.0 – Drawing Diverse Samples from RNA-Seq Libraries

VARUS 1.0.0

:: DESCRIPTION

VARUS automates the selection and download of a limited number of RNA-seq reads from at NCBI’s Sequence Read Archive (SRA) targeting a sufficiently high coverage for many genes for the purpose of gene-finder training and genome annotation.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

VARUS

:: MORE INFORMATION

Citation

Stanke M, Bruhn W, Becker F, Hoff KJ.
VARUS: sampling complementary RNA reads from the sequence read archive.
BMC Bioinformatics. 2019 Nov 8;20(1):558. doi: 10.1186/s12859-019-3182-x. PMID: 31703556; PMCID: PMC6842140.

BRAKER v2.1.6 – RNA-seq based Eukaryotic Genome Annotation pipeline

BRAKER v2.1.6 / TSEBRA v1.0.3

:: DESCRIPTION

BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS

TSEBRA (Transcript Selector for BRAKER) is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

BRAKER / TSEBRA

:: MORE INFORMATION

Citation

Gabriel L, Hoff KJ, Brůna T, Borodovsky M, Stanke M.
TSEBRA: transcript selector for BRAKER.
BMC Bioinformatics. 2021 Nov 25;22(1):566. doi: 10.1186/s12859-021-04482-0. PMID: 34823473.

Brůna T, Hoff KJ, Lomsadze A, Stanke M, Borodovsky M.
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.
NAR Genom Bioinform. 2021 Jan 6;3(1):lqaa108. doi: 10.1093/nargab/lqaa108. PMID: 33575650; PMCID: PMC7787252.

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M.
Bioinformatics. 2015 Nov 11. pii: btv661

NorahDesk 1.4 – Detecting small non-coding RNA(ncRNA) from Deep Sequencing data (RNA-seq)

NorahDesk 1.4

:: DESCRIPTION

NorahDesk is a small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data. NorahDesk utilizes the coverage-distribution of small RNA sequence data and thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes.

::DEVELOPER

NorahDesk team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Vienna RNA

:: DOWNLOAD

NorahDesk

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep;40(16):7633-43. doi: 10.1093/nar/gks505.
Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.
Ragan C, Mowry BJ, Bauer DC.

AStalavista 4.0.1 – Alternative Splicing Transcriptional Landscape Visualization tool

AStalavista 4.0.1

:: DESCRIPTION

AStalavista (the Alternative Splicing Trascriptional Landscape Visualization Tool) retrieves all alternative splicing events from generic transcript annotations.

::DEVELOPER

RODERIC GUIGO LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX/Windows
Java

:: DOWNLOAD

AStalavista

:: MORE INFORMATION

Citation

Sammeth M, Foissac S, Guigó R (2008)
A General Definition and Nomenclature for Alternative Splicing Events.
PLoS Comput Biol 4(8): e1000147.

Grape 1.1.0 – Pipeline for Processing and Analyzing RNA-Seq data

Grape 1.1.0

:: DESCRIPTION

The Grape RNAseq Analysis Pipeline Environment implements a set of workflows that allow for easy exploration of RNA-Seq data.

::DEVELOPER

Guigo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Grape

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 1;29(5):614-21. doi: 10.1093/bioinformatics/btt016. Epub 2013 Jan 17.
Grape RNA-Seq analysis pipeline environment.
Knowles DG, Röder M, Merkel A, Guigó R.

get_size_NN v1 – Neutral Network Size Estimation

get_size_NN v1

:: DESCRIPTION

get_size_NN calculates, via nested Monte Carlo, an estimate of the size of the neutral set (network) of a given RNA secondary structure.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

get_size_NN

:: MORE INFORMATION

Citation:

Thomas Jörg, Olivier C Martin and Andreas Wagner
Neutral network sizes of biological RNA molecules can be computed and are atypically large.
BMC Bioinformatics 2008, 9:464

ViennaRNA 2.5.0 – RNA Secondary Structure Prediction & Comparison

ViennaRNA 2.5.0

:: DESCRIPTION

ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Vienna RNA WebServers

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Mac OsX/ Windows

:: DOWNLOAD

Vienna RNA

:: MORE INFORMATION

Citation

Methods Mol Biol. 2015;1269:307-26. doi: 10.1007/978-1-4939-2291-8_19.
The ViennaRNA web services.
Gruber AR1, Bernhart SH, Lorenz R.

Ivo L. Hofacker
Vienna RNA secondary structure serverNucl.
Acids Res. (2003) 31 (13): 3429-3431

Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.
ViennaRNA Package 2.0
Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26

Scirpy v0.10.1 – Scanpy Extension for analyzing Single-cell T-cell Receptor-sequencing data

Scirpy v0.10.1

:: DESCRIPTION

Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.

::DEVELOPER

the Institute of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Scirpy

:: MORE INFORMATION

Citation

Sturm G, Szabo T, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F.
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data.
Bioinformatics. 2020 Sep 15;36(18):4817-4818. doi: 10.1093/bioinformatics/btaa611. PMID: 32614448; PMCID: PMC7751015.