Category: RNA Analysis

RNAML 1.1.2 – Syntax for Exchanging RNA Information

RNAML 1.1.2

:: DESCRIPTION

RNAML is a standard syntax for exchanging RNA information.This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots

::DEVELOPER

 Laboratoire de Bioinformatique Théorique

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Java 

:: DOWNLOAD

 RNAML

:: MORE INFORMATION

Citation

A. Waugh et al.
RNAML: a standard syntax for exchanging RNA information.
RNA. 2002 Jun;8(6):707-17.

Randfold 2.0 – RNA Minimum Free Energy of Folding Randomization Test

Randfold 2.0

:: DESCRIPTION

Randfold compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.

:: DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Randfold

:: MORE INFORMATION

Citation:

Bonnet, E., * Wuyts, J., Rouzé, P., Van de Peer, Y. (2004)
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.
Bioinformatics 20, 2911-7

MIRO 2.9 – Analyze microRNAs using Next-generation Sequencing Data

MIRO 2.9

:: DESCRIPTION

The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

::DEVELOPER

MIRO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Perl

:: DOWNLOAD

 MIRO

:: MORE INFORMATION

SPLITS 1.1 / SPLITSX – tRNA Detection in Genome Sequence

SPLITS 1.1 / SPLITSX

:: DESCRIPTION

SPLITS and SPLITSX, expansion programs for tRNAscan-SE to detect spliced-tRNA genes, such as split-tRNA genes (Figure A) and intron-containing tRNA genes (Figure B) in archaea.

The length of the query sequence should be limited within 5 mega base pairs (nucleotide). If your sequence is longer than this, please divide the sequence and submit separately. Finally these programs are under active development. If you use these programs, please help me out by e-mailing me with suggestions, comments, and bug reports.

::DEVELOPER

Institute for Advanced Biosciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

 SPLITS  / SPLITSX

:: MORE INFORMATION

Citation

Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, Kanai A. (2006).
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.
In Silico Biology. 6, 0039.

Sugahara J., Yachie N., Arakawa K., Tomita M. (2007)
In Silico Screening of Archaeal tRNA-encoding Genes Having Multiple Introns with Bulge-Helix-Bulge Splicing Motifs,
RNA; 13: 671-681

Erpin 5.5.4 – RNA Motif Search program

Erpin 5.5.4

:: DESCRIPTION

ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

::DEVELOPER

Daniel GAUTHERET and André Lambert

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Erpin

:: MORE INFORMATION

Citation

Gautheret D, Lambert A. (2001)
Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles.
J Mol Biol. 313:1003-11

Darn 1.0 – Non-protein-coding RNA Detection

Darn 1.0

:: DESCRIPTION

Darn is a RNA motif search tool. It finds all the subsequences that match a specified motif on some input genomic sequence(s).Darn uses a weighted constraint solver to localize the portions of a genomic sequence that match a motif. The motif is expressed in a specific language (see section 5). Some motif descriptors are provided with the software for FMN, Lysine, RNaseP, SAM,snoRNA C/D-box and tRNA search.

::DEVELOPER

Matthias Zytnicki 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Darn

:: MORE INFORMATION

Citation

M. Zytnicki, C. Gaspin, T. Schiex.
Darn – A Weighted Constraint Solver for RNA Motif Localization.
Constraints, Volume 13 (2008).

MEMERIS 1.0 – MEME in Rna’s Including Secondary Structures

MEMERIS 1.0

:: DESCRIPTION

MEMERIS (Muptiple Em for Motif Elucidation in Rna’s Including Secondary Structures) integrates information about RNA secondary structures into the motif search to guide the search towards single-stranded regions.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MEMERIS

:: MORE INFORMATION

Citation

Hiller M, Pudimat R, Busch A, and Backofen R.
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions.
Nucleic Acids Res. 2006

LocalFold 1.0 – Local Folding of RNA

LocalFold 1.0

:: DESCRIPTION

LocalFold is a modification of the RNAplfold local folding algorithm. LocalFold only considers base-pairs centred within a window such that (i,j) are not located within the first and last positions of the windows.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LocalFold

:: MORE INFORMATION

Citation

Sita J. Lange, Daniel Maticzka, Mathias Möhl, Joshua N. Gagnon, Chris M. Brown and Rolf Backofen
Global or local? Predicting secondary structure and accessibility in mRNAs

RNAsoup 1.0a – Structural Clustering Pipeline for Structured RNAs

RNAsoup 1.0a

:: DESCRIPTION

RNAsoup  (Spot grOUPs in RNA cluster-tree) is a post-processing tool of a structural clustering pipeline for structured RNAs (e.g. RNAclust). It requires as input a binary cluster-tree, the minimum free energy (MFE) of the consensus secondary structure for each internal node, and a FASTA file of the input sequences. It detects the optimal partition (i.e. finding the optimal number of clusters/groups) into distinct subtrees where each subtree contains structurally related RNA sequences. RNAsoup is based on a decision rule which evaluates the squared error from the minimum free energies of the single sequences to the minimum free energy of the consensus secondary structure.

::DEVELOPER

Kristin Reiche

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAsoup

:: MORE INFORMATION

RNAstrand 2.0.0 – Predict Reading Direction of Structured RNAs in Multiple Sequence Alignments

RNAstrand 2.0.0

:: DESCRIPTION

RNAstrand predicts the reading direction of a structured RNA gene from a multiple sequence alignment and its reverse complement. It is meant as a post processing tool for RNA prediction tools which in general do not reliable annotate the reading direction of the structured RNA candidate.

RNAstrand Online Version

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RNAstrand

:: MORE INFORMATION

Citation

RNAstrand: Reading direction of structured RNAs in multiple sequence alignments
Kristin Reiche, Peter F. Stadler,
Algorithms for Molecular Biology, 2:6, 2007.