HALO 1.3 – Precise RNA de novo Transcript Half-life Determination

HALO 1.3

:: DESCRIPTION

HALO (Half-life Organizer) is the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription. In addition, methods for quality control, filtering and normalization are supplied. HALO provides a graphical user interface, command line tools and a well-documented Java API. Thus, it can be used both by biologists to determine transcript half-lives fast and reliably with the user interfaces provided as well as software developers integrating transcript half-life analysis into other gene expression profiling pipelines.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

HALO

:: MORE INFORMATION

Citation

Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer.
HALO – A Java framework for precise transcript half-life determination.
Bioinformatics, vol 26, no. 9, pp. 1264-1266, May 2010.

RNA-DV 1.0 – Design & Visualization Tool for RNA Secondary Structure

RNA-DV 1.0

:: DESCRIPTION

RNA-DV (RNA Design & Visualization) is a flexible and powerful tool targeted at visualization and modification of RNA secondary structure. Compare to existing software applications, RNA-DV set itself apart by not only providing an editing and visualization interface but also integrates thermodynamic energies for the current structure design. RNA-DV aims at providing an easy-to-use GUI for visualizing and designing RNA secondary structures. It allows users to interact directly with the RNA structure and perform operations such as changing primary sequence content and connect/disconnect nucleotide bonds. It also integrates thermodynamic energy calculations including four major energy models. RNA-DV recognizes three input formats including CT, RNAML and dot bracket (dp).

::DEVELOPER

Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

RNA-DV

:: MORE INFORMATION

PicXAA 1.03 / PicXAA-R 1.0 – Probabilistic Maximum Accuracy Alignment / for RNA Structural Alignment

PicXAA 1.03 / PicXAA-R 1.0

:: DESCRIPTION

PicXAA is a probabilistic non-progressive alignment algorithm that finds protein multiple sequence alignments with maximum expected accuracy.

PicXAA-R is an extension of PicXAA for greedy structural alignment of NonCoding RNAs.

::DEVELOPER

Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PicXAA / PicXAA-R

:: MORE INFORMATION

Citation

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
Nucleic Acids Research, 38(15):4917-4928, 2010.

PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
BMC Bioinformatics, 12(Suppl 1):S38, 2011

Knotted2Nested – Remove Pseudoknots from RNA

Knotted2Nested

:: DESCRIPTION

Knotted2Nested removes pseudoknots from a list of RNA base pairs, using different algorithms. It produces in pseudoknot-free (dot-bracket) 2D structures.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python

:: DOWNLOAD

Knotted2Nested

:: MORE INFORMATION

Citation

Sandra Smit, Kristian Rother, Jaap Heringa, and Rob Knight.
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
RNA (2008) 14(3):410-416.

Suitename 0.3 – RNA Conformer

Suitename 0.3

:: DESCRIPTION

Suitename is a new C program that supports the ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development

From dihedral-angle input for a specific RNA structure (usually from Dangle), Suitename categorizes the RNA backbone geometry of each suite (the sugar-to-sugar version of a residue) either as an outlier (“!!”) or as belonging to one of the 53 defined conformer bins.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows / Mac / Linux

:: DOWNLOAD

Suitename

:: MORE INFORMATION

Suitename is free software available under the terms of its own BSD-style license.

RNABC 1.11 – RNA Backbone Correction

RNABC 1.11

:: DESCRIPTION

RNABC (RNA Backbone Correction) is designed for reducing the steric clashes in dinucleotides of existing RNA backbone structures. It first fixes the phosphate and base positions, which are the clearest parts in X-ray crystallography structure, and then reconstructs the remaining atoms of the dinucleotide using forward kinematics and conjugate gradient method. The input parameters, like bond lengths, bond angles, and sugar pucker types, are from canonical values or specified by users. The output results cluster the possible suite conformations (from base to base) without steric clashes.

::DEVELOPER

Xueyi Wang & Prof. Jack Snoeyink
Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows / Mac / Linux

:: DOWNLOAD

RNABC

:: MORE INFORMATION

RNABC is described in X. Wang, G. Kapral, L. Murray, D. Richardson, J. Richardson & J. Snoeyink. “RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone”. Journal Mathematical Biology (published January 2008, doi: 10.1007/s00285-007-0082)

RNABC is free software available under the terms of its own BSD-style license.