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.

RIscoper – RNA Interaction Extraction from Literatures

RIscoper

:: DESCRIPTION

RIscoper (RNA Interactome Scoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model.

::DEVELOPER

WD Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

RIscoper

:: MORE INFORMATION

Citation

Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J.
RIscoper: a tool for RNA-RNA interaction extraction from the literature.
Bioinformatics. 2019 Sep 1;35(17):3199-3202. doi: 10.1093/bioinformatics/btz044. PMID: 30668649.

SimRNA 3.20 – Simulations of RNA Conformational Dynamics

SimRNA 3.20

:: DESCRIPTION

SimRNA is a tool for simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and its applications include RNA 3D structure prediction.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SimRNA

:: MORE INFORMATION

Citation

Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM.
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Nucleic Acids Res. 2016 Apr 20;44(7):e63. doi: 10.1093/nar/gkv1479. Epub 2015 Dec 19. PMID: 26687716; PMCID: PMC4838351.

RNAstructure 6.3 – Prediction & Analysis of RNA Secondary Structure

RNAstructure 6.3

:: DESCRIPTION

RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.

::DEVELOPER

Mathews Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

RNAstructure

:: MORE INFORMATION

Citation

AccessFold: Predicting RNA-RNA Interactions with Consideration for Competing Self-Structure.
DiChiacchio L, Sloma MF, Mathews DH.
Bioinformatics. 2015 Nov 20. pii: btv682.

Reuter, J. S., & Mathews, D. H. (2010).
RNAstructure: software for RNA secondary structure prediction and analysis.
BMC Bioinformatics. 11,129.

jViz.Rna 4.0 – Visual Comparison of RNA Secondary Structure

jViz.Rna 4.0

:: DESCRIPTION

jViz.Rna is a multi-platform visualization tool capable of displaying and comparing RNA secondary structures encoded in a number of file formats. Structures can be shown using six different visualization modes including a numerical analysis mode which includes sensitivity and specificity. Any of the drawings and data produced can be saved in a variety of formats enabling easy usage in publications and presentations.

::DEVELOPER

jViz.Rna Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 jViz.Rna

:: MORE INFORMATION

Citation:

Shabash B, Wiese KC.
jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs.
PLoS One. 2019 May 6;14(5):e0210281. doi: 10.1371/journal.pone.0210281. PMID: 31059508; PMCID: PMC6502502.

Kay C. Wiese and Edward Glen (2006),
jViz.Rna – An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots
Proceedings of the 19th International Symposium on Computer Based Medical Systems (IEEE/CBMS-2006), June 2006, pp 659-664.

ERD – Evolutionary RNA Designer

ERD

:: DESCRIPTION

ERD designs sequences that fold into a given target RNA secondary structure, i.e. whose minimum free energy (MFE) structure is the target structure.

::DEVELOPER

ERD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ERD

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1250-8. doi: 10.1093/bioinformatics/btu001. Epub 2014 Jan 8.
Evolutionary solution for the RNA design problem.
Esmaili-Taheri A1, Ganjtabesh M, Mohammad-Noori M.

HDOCK 1.1 – Protein-protein and Protein-DNA/RNA Docking based on Hybrid Strategy

HDOCK 1.1

:: DESCRIPTION

The HDOCK server is to predict the binding complexes between two molecules like proteins and nucleic acids by using a hybrid docking strategy.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HDOCK 

:: MORE INFORMATION

Citation:

Yan Y, Zhang D, Zhou P, Li B, Huang SY.
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.
Nucleic Acids Res. 2017 Jul 3;45(W1):W365-W373. doi: 10.1093/nar/gkx407. PMID: 28521030; PMCID: PMC5793843.

RNAHeliCes 2.0.14 – RNA Folding Space Analysis

RNAHeliCes 2.0.14

:: DESCRIPTION

RNAHeliCes is a tool for RNA folding space analysis. It abstracts from structural detail and maps structures using a position-specific abstraction based on helices.

::DEVELOPER

Cyanolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 RNAHeliCes

:: MORE INFORMATION

Citation:

RNA. 2012 Dec;18(12):2135-47. doi: 10.1261/rna.033548.112. Epub 2012 Oct 25.
Abstract folding space analysis based on helices.
Huang J1, Backofen R, Voß B.

Pse-in-One 1.0.6 – Generating various modes of Pseudo Components of DNA, RNA and Protein Sequences

Pse-in-One 1.0.6

:: DESCRIPTION

Pse-in-One is a web server for generating various modes of pseudo components of DNA, RNA and protein sequences

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pse-in-One

:: MORE INFORMATION

Citation

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
Liu B, Liu F, Wang X, Chen J, Fang L, Chou KC.
Nucleic Acids Res. 2015 Jul 1;43(W1):W65-71. doi: 10.1093/nar/gkv458.