FRUUT 2.46 – Fast RNA Unrooted Unordered Tree Alignment

FRUUT 2.46

:: DESCRIPTION

FRUUT computes an RNA structure alignment of two given RNA molecules. We generalize previous algorithms that either solved the problem in an asymmetric manner, or were restricted to the rooted and/or ordered cases. Focusing here on the most general unrooted unordered case, we show that our algorithm has an O(nTnS min(dT, dS)) time complexity, where nT and nS are the number of nodes and dT and dS are the maximum node degrees in the input trees T and S, respectively. This maintains (and slightly improves) the time complexity of previous, less general algorithms for the problem.

::DEVELOPER

Michal Ziv-Ukelson’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

 FRUUT

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2013 Apr 16;8(1):13. doi: 10.1186/1748-7188-8-13.
Unrooted unordered homeomorphic subtree alignment of RNA trees.
Milo N1, Zakov S, Katzenelson E, Bachmat E, Dinitz Y, Ziv-Ukelson M.

Context Fold 1.0 – RNA Secondary Structure Prediction tool

Context Fold 1.0

:: DESCRIPTION

Context Fold is an RNA secondary structure prediction tool. It applies feature-rich scoring models, whose parameters were obtained after training on comprehensive datasets.

::DEVELOPER

Michal Ziv-Ukelson’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

 Context Fold

:: MORE INFORMATION

Citation

Shay Zakov, Yoav Goldberg, Michael Elhadad and Michal Ziv-Ukelson.
Rich Parameterization Improves RNA Structure Prediction
Journal of Computational Biology, November 2011, 18(11): 1525-1542. doi:10.1089/cmb.2011.0184.

ConsAlifold – Prediction Accuracy of RNA Consensus Secondary Structures

ConsAlifold

:: DESCRIPTION

ConsAlifold is a dynamic programming-based method that predicts the consensus secondary structure of an RNA sequence alignment.

::DEVELOPER

ConsAlifold team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

ConsAlifold

:: MORE INFORMATION

Citation

Tagashira M, Asai K.
ConsAlifold: Considering RNA Structural Alignments Improves Prediction Accuracy of RNA Consensus Secondary Structures.
Bioinformatics. 2021 Oct 25:btab738. doi: 10.1093/bioinformatics/btab738. Epub ahead of print. PMID: 34694364.

EditPredict – Prediction of RNA editable sites with convolutional Neural network

EditPredict

:: DESCRIPTION

EditPredict is a sequence-only, sequencing-independent tool, which can be used stand-alone to predict novel RNA editing and to assist in filtering for candidate RNA editing detected from RNA-Seq data.

::DEVELOPER

Steven Wong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

EditPredict

:: MORE INFORMATION

Citation

Wang J, Ness S, Brown R, Yu H, Oyebamiji O, Jiang L, Sheng Q, Samuels DC, Zhao YY, Tang J, Guo Y.
EditPredict: Prediction of RNA editable sites with convolutional neural network.
Genomics. 2021 Sep 23;113(6):3864-3871. doi: 10.1016/j.ygeno.2021.09.016. Epub ahead of print. PMID: 34562567.

RateLimit – Rate Limiting Steps in Transcription from RNA production times in live cells

RateLimit

:: DESCRIPTION

RateLimit is a tool to identify rate limiting steps in transcription from RNA production times in live cells.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

RateLimit

:: MORE INFORMATION

Citation:

Häkkinen A, Ribeiro AS.
Characterizing rate limiting steps in transcription from RNA production times in live cells.
Bioinformatics. 2016 May 1;32(9):1346-52. doi: 10.1093/bioinformatics/btv744. Epub 2015 Dec 31. PMID: 26722120.

iPARTS 2 – A Tool of Improved/ Pairwise Alignment of RNA Tertiary Structures

iPARTS2

:: DESCRIPTION

iPARTS2 (improved PARTS) is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach.

::DEVELOPER

Chih-Wei Wang, Kun-Tze Chen and Chin Lung Lu.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yang CH, Shih CT, Chen KT, Lee PH, Tsai PH, Lin JC, Yen CY, Lin TY, Lu CL.
iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.
Nucleic Acids Res. 2016 Jul 8;44(W1):W328-32. doi: 10.1093/nar/gkw412. Epub 2016 May 16. PMID: 27185896; PMCID: PMC4987943.

iPARTS: an improved tool of pairwise alignment of RNA tertiary structures.
Wang CW, Chen KT, Lu CL.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W340-7. doi: 10.1093/nar/gkq483.

Galaxy RNA workbench 19.01 – The RNA Analyses Workbench

Galaxy RNA workbench 19.01

:: DESCRIPTION

The RNA Galaxy workbench is a comprehensive set of analysis tools and consolidated workflows. The workbench is based on the Galaxy framework, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.

::DEVELOPER

the de.NBI RNA Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Galaxy RNA workbench

:: MORE INFORMATION

Citation

Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R.
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409. PMID: 28582575; PMCID: PMC5570170.

RNAlign2D – Multiple Sequence Alignment of RNA using MUSCLE and Secondary Structure data

RNAlign2D

:: DESCRIPTION

RNAlign2D is a Python wrapper allowing one to align multiple RNA molecules using information about secondary structure and sequence. For this purpose MUSCLE program is used, but one can adjust it to use any other multiple sequence alignment tool.

::DEVELOPER

RNA Bioscience Initiative

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • MUSCLE

:: DOWNLOAD

RNAlign2D

:: MORE INFORMATION

Citation

Woźniak T, Sajek M, Jaruzelska J, Sajek MP.
RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix.
BMC Bioinformatics. 2021 Oct 16;22(1):504. doi: 10.1186/s12859-021-04426-8. PMID: 34656080; PMCID: PMC8520625.

BioSeq-Analysis 2.0 / BioSeq-BLM 1.0 – Analyzing DNA, RNA, and Protein Sequences based on Biological Language Models

 BioSeq-Analysis 2.0 / BioSeq-BLM 1.0

:: DESCRIPTION

BioSeq-Analysis is an platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches

BioSeq-BLM is a platform for analyzing DNA, RNA, and protein sequences based on biological language models

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

BioSeq-Analysis / BioSeq-BLM

:: MORE INFORMATION

Citation

Li HL, Pang YH, Liu B.
BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models.
Nucleic Acids Res. 2021 Sep 28:gkab829. doi: 10.1093/nar/gkab829. Epub ahead of print. PMID: 34581805.

Liu B, Gao X, Zhang H.
BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches.
Nucleic Acids Res. 2019 Nov 18;47(20):e127. doi: 10.1093/nar/gkz740. PMID: 31504851; PMCID: PMC6847461.

CICERO v1.8.1 – Clipped-reads Extended for RNA Optimization

CICERO v1.8.1

:: DESCRIPTION

CICERO is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

CICERO

:: MORE INFORMATION

Citation

Tian L, Li Y, Edmonson MN, Zhou X, Newman S, McLeod C, Thrasher A, Liu Y, Tang B, Rusch MC, Easton J, Ma J, Davis E, Trull A, Michael JR, Szlachta K, Mullighan C, Baker SJ, Downing JR, Ellison DW, Zhang J.
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
Genome Biol. 2020 May 28;21(1):126. doi: 10.1186/s13059-020-02043-x. PMID: 32466770; PMCID: PMC7325161.

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