ProbeAlign 0.3 – ncRNA Homology Search

ProbeAlign 0.3

:: DESCRIPTION

ProbeAlign is a program for annotating ncRNA structures by incorporating high-throughput sequencing based structure probing information.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ProbeAlign

:: MORE INFORMATION

Citation:

ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.
Ge P, Zhong C, Zhang S.
BMC Bioinformatics. 2014;15 Suppl 9:S15. doi: 10.1186/1471-2105-15-S9-S15.

RNAcon 1.0 – Classification of non-coding RNAs (ncRNA)

RNAcon 1.0

:: DESCRIPTION

RNAcon is a web-server for the prediction and classification of non-coding RNAs. It uses SVM-based model for the discrimination between coding and ncRNAs and RandomForest-based prediction model for the classification of ncRNAs into different classes. The structural information based graph properties were used for the development of prediction model.

::DEVELOPER

RNAcon team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAcon

:: MORE INFORMATION

Citation

Panwar, B; Arora, A. and Raghava GP (2014)
Prediction and classification of ncRNAs using structural information
BMC Genomics 2014, 15:127

nocoRNAc 1.23 – Predict & Characterise ncRNA Transcripts in Bacteria

nocoRNAc 1.23

:: DESCRIPTION

nocoRNAc (non-coding RNA characterization) is a Java program for the prediction and characterization of ncRNA transcripts in bacteria. nocoRNAc takes the coordinates of putative ncRNA loci as input and annotates them with transcriptional features to conduct strand-specific transcript predictions. Our approach is not limited to intergenic regions but also applied to predict cis-encoded asRNA transcripts. For the detection of the transcript’s 3′ end nocoRNAc integrates the program TransTermHP (Kingsford et al., 2007) to predict Rho-independent terminator signals. The 5′ start is predicted by the detection of destabilized regions in the genomic DNA. For this purpose we implemented the so-called SIDD model (Benham, Bi, 2004), which has been shown to be applicable to the detection of promoter regions in microbial genomes. Therefore, nocoRNAc does not have to rely on information about known TFBS. The putative transcriptional features are then combined to classify ncRNA loci into either being an ncRNA transcript or not. For ncRNAs that are classified as transcripts the strand is automatically specified, and its boundaries are derived from the SIDD sites and the Rho-independent transcription termination signal. Those loci that are classified not to be a transcript might be false positive predictions or they contain cis-regulatory motifs. For the latter, nocoRNAc incorporates other functionalities for the further analysis of the ncRNA loci such as the search for known RNA motifs from the Rfam database. Furthermore, nocoRNAc provides methods for the prediction of RNA-RNA interactions between ncRNAs and mRNAs. All results can be studied in detail in nocoRNAc’s integrated interactive R environment.

::DEVELOPER

Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

nocoRNAc

:: MORE INFORMATION

Citation

nocoRNAc: Characterization of non-coding RNAs in prokaryotes
Alexander Herbig, Kay Nieselt
BMC Bioinformatics. 2011 Jan 31;12:40. doi: 10.1186/1471-2105-12-40.

RandA 1.1.4 – ncRNA Profiling

RandA 1.1.4

:: DESCRIPTION

RandA (ncRNA Read-and-Analyze) allows to analyze all known non-coding RNAs in a cell.

::DEVELOPER

Team Shomron

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R
  • Java

:: DOWNLOAD

 RandA

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jun;40(11):e86. doi: 10.1093/nar/gks228. Epub 2012 Mar 9.
Novel insight into the non-coding repertoire through deep sequencing analysis.
Isakov O1, Ronen R, Kovarsky J, Gabay A, Gan I, Modai S, Shomron N.

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.

ApolloRNA 1.11.8 – Apollo for non Protein Coding RNA (ncRNA) Identification

ApolloRNA 1.11.8

:: DESCRIPTION

ApolloRNA is an extension for ncRNA identification of the Apollo environment , a genome annotation viewer and editor.

::DEVELOPER

the Biometry and Artificial Intelligence Laboratory of INRA Toulouse, France

:: SCREENSHOTS

ApolloRNA

:: REQUIREMENTS

:: DOWNLOAD

 ApolloRNA

:: MORE INFORMATION

Citation:

Cros MJ, Moisan A, Cierco-Ayrolles C, Gaspin C.
Visualizing and exploring genomic information for non-protein-coding RNA identification using ApolloRNA.
Nature Protocols. (2007) doi: 10.1036/nprot.20.07.285.

Chain-RNA 20120225 – Comparative ncRNA Search Tool Based on the Two-dimensional Chain Algorith

Chain-RNA 20120225

:: DESCRIPTION

Chain-RNA is an ncRNA structural alignment program based on extended two-dimensional chain algorithm. It has been applied to pairwise genome-scale ncRNA search.

::DEVELOPER

Jikai Lei, Yanni Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Chain-RNA

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Oct 30. [Epub ahead of print]
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-dimensional Chain Algorithm.
Lei J, Techa-Angkoon P, Sun Y.

Grammar String – novel ncRNA Secondary Structure Representation

Grammar String

:: DESCRIPTION

Grammar String is a novel representation of noncoding RNA secondary structure. By encoding both the sequence and secondary structure of ncRNAs in a string, ncRNA structural alignment is converted to sequence alignment. The software package provides an ncRNA consensus secondary structure derivation tool.

There are three sub-programs
1. ct2ss: The program to convert .ct file to secondary structure
2. ss2gs: The program to generate grammar string from sequence and structure
3. msa: The alignment program, pair-wise and multiple alignment program

::DEVELOPER

Yanni Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Grammar String

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2011 Apr;9(2):317-37.
ncRNA consensus secondary structure derivation using grammar strings.
Achawanantakun R, Sun Y, Takyar SS.

PORTRAIT 1.2 – Prediction of transcriptomic ncRNA by ab initio methods

PORTRAIT 1.2

:: DESCRIPTION

PORTRAIT (acronym for Prediction of transcriptomic ncRNA by ab initio methods) is an algorithm for identifying non-coding RNAs on a transcriptome context.

::DEVELOPER

Roberto Arrial ,Roberto Togawa

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PORTRAIT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Aug 4;10:239. doi: 10.1186/1471-2105-10-239.
Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis.
Arrial RT, Togawa RC, Brigido Mde M.