Tag: RNA Alignment

BoulderALE 1.0.0 – Web-based RNA Alignment Tool

BoulderALE 1.0.0

:: DESCRIPTION

BoulderALE (Boulder Alignment Editor) is an RNA alignment editor, which allows for the annotation of Watson-Crick and non-Watson-Crick basepairs, annotation of features (i.e. stems, loops, etc.), collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences (using VARNA ) and base composition given a secondary structure (using KiNG).

::DEVELOPER

Knight Lab

:: SCREENSHOT

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Apache/ModPython
  • Python
  • Numpy
  • PyCogent
  • Kinemage Scripts

:: DOWNLOAD

 BoulderALE 

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1706-7. doi: 10.1093/bioinformatics/btr258.
Boulder ALignment Editor (ALE): a web-based RNA alignment tool.
Stombaugh J, Widmann J, McDonald D, Knight R.

Infernal 1.1.4 – Inference of RNA Alignment

Infernal 1.1.4

:: DESCRIPTION

Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

::DEVELOPER

Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Infernal

:: MORE INFORMATION

Citation

E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy
Infernal 1.0: Inference of RNA alignments
Bioinformatics 25:1335-1337 (2009), .

PhyloRNAalifold v1 – Predicting Consensus Structures in RNA Alignments by incorporating RNAalifold with Phylogenetic information

PhyloRNAalifold v1

:: DESCRIPTION

PhyloRNAalifold is a program for predicting consensus structures of aligned RNA sequences by incorporating phylogetetic-based covarying mutations.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PhyloRNAalifold

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Apr 27;14:142. doi: 10.1186/1471-2105-14-142.
Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction.
Ge P, Zhang S.