CCmiR – Prediction of miRNA Competitive / Cooperative Binding

CCmiR

:: DESCRIPTION

CCmiR is a software for competitive and cooperative microRNA binding prediction

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

CCmiR

:: MORE INFORMATION

Citation:

Bioinformatics. 2018 Jan 15;34(2):198-206. doi: 10.1093/bioinformatics/btx606.
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction.
Ding J, Li X, Hu H.

miRModule – Identification of miRNA modules from high-throughput miRNA-mRNA Binding Experiments

miRModule

:: DESCRIPTION

MiRModule is a software tool for systematic discovery of miRNA modules from a set of predefined miRNA target sites. Given a sets of miRNA binding sites, miRModule efficiently identifies groups of miRNAs, whose binding sites significantly co-occur in the same set of target mRNAs, as putative miRNA modules. It works for both experimentally determined miRNA-mRNA binding sites (e.g. from CLASH) and computationally predicted miRNA-mRNA binding sites (e.g. from miRanda).

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 MiRModule

:: MORE INFORMATION

Citation

MicroRNA modules prefer to bind weak and unconventional target sites.
Ding J, Li X, Hu H.
Bioinformatics. 2014 Dec 18. pii: btu833.

TarPmiR – microRNA Target Site Prediction

TarPmiR

:: DESCRIPTION

TarPmiR is a miRNA-mRNA binding sites prediction tool, which can utilize miRNA-mRNA binding experiment data such as CLASH (cross-linking ligation and sequencing of hybrids) .

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows
  • Python

:: DOWNLOAD

 TarPmiR

:: MORE INFORMATION

Citation:

TarPmiR: a new approach for microRNA target site prediction.
Ding J, Li X, Hu H.
Bioinformatics. 2016 May 20. pii: btw318.

CROSS / CROSSalign / CROSSalive – Recognition of RNA Secondary Structure

CROSS / CROSSalign / CROSSalive

:: DESCRIPTION

CROSS predicts the secondary structure propensity profile of an RNA molecule at single-nucleotide resolution. CROSS produces a table with the propensity scores and a graphical representation of the profile.

CROSSalign computes the similarity of RNA secondary structure

CROSSalive computes the structure of RNA molecules in vivo. Changes of structure upon N6-Methyladenosine methylation can be predicted.

::DEVELOPER

Tartaglia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CROSSalive: a web server for predicting the in vivo structure of RNA molecules.
Delli Ponti R, Armaos A, Vandelli A, Tartaglia GG.
Bioinformatics. 2019 Aug 28. pii: btz666. doi: 10.1093/bioinformatics/btz666.

Front Mol Biosci. 2018 Dec 3;5:111. doi: 10.3389/fmolb.2018.00111. eCollection 2018.
A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs.
Delli Ponti R, Armaos A, Marti S, Tartaglia GG

A high-throughput approach to profile RNA structure.
Delli Ponti R, Marti S, Armaos A, Tartaglia GG.
Nucleic Acids Res. 2017 Mar 17;45(5):e35. doi: 10.1093/nar/gkw1094.

Quantas 1.0.9 – Analyze alternative Splicing using RNA-Seq

Quantas 1.0.9

:: DESCRIPTION

Quantas includes a package to infer transcript structure from paired-end RNA-seq data (gapless), and a package to count RNA-seq reads for each alternative splicing isoform (countit).

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl 

:: DOWNLOAD

 Quantas

:: MORE INFORMATION

mRIN 1.2.0 – direct Assessment of mRNA integrity from RNA-Seq data

mRIN 1.2.0

:: DESCRIPTION

mRIN (mRNA integrity number) is a computational method to assess a quantitative measure of mRNA integrityta. This is done by quantitatively modeling of the 3′ bias of read coverage profiles along each mRNA transcript. A per-sample summary mRIN is then derived as an indicator of mRNA degradation. This method has been used for systematic analysis of large scale RNA-Seq data of postmortem tissues, in which RNA degradation during tissue collection is particularly an issue.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl 

:: DOWNLOAD

mRIN

:: MORE INFORMATION

Citation

Nat Commun. 2015 Aug 3;6:7816. doi: 10.1038/ncomms8816.
mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.
Feng H, Zhang X, Zhang C

OLego 1.1.7 – Senstive and fast Splice Mapping for mRNA-seq reads

OLego 1.1.7

:: DESCRIPTION

OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 OLego

:: MORE INFORMATION

Citation

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.
Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C.
Nucleic Acids Res. 2013 Apr 9.

RNAMotif 3.1.1 – Find Structural Motifs in RNA

RNAMotif 3.1.1

:: DESCRIPTION

The rnamotif program searches a database for RNA sequences that match a “motif” describing secondary structure interactions. A match means that the given sequence is capable of adopting the given secondary structure, but is not intended to be predictive. Matches can be ranked by applying scoring rules that may provide finer distinctions than just matching to a profile.

::DEVELOPER

the Case group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window with Cygwin / Linux / Mac OsX
  • C-compiler

:: DOWNLOAD

RNAMotif

:: MORE INFORMATION

Citation

T. Macke, D. Ecker, R. Gutell, D. Gautheret, D.A. Case and R. Sampath.
RNAMotif — A new RNA secondary structure definition and discovery algorithm.
Nucl. Acids Res. 29, 4724-4735 (2001).

CTK v1.1.3 – CLIP Tool Kit, previously known as CIMS

CTK v1.1.3

:: DESCRIPTION

CTK (the CLIP Tool Kit) is a software package that provides a set of tools for analysis of CLIP data starting from the raw reads generated by the sequencer. It includes pipelines to filter and map reads, collapse PCR duplicates to obtain unique CLIP tags, define CLIP tag clusters and call peaks, and define the exact protein-RNA crosslink sites by CIMS and CITS analysis. This software package is an expanded version of our previous CIMS package.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl 

:: DOWNLOAD

CTK

:: MORE INFORMATION

Citation

CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
Shah A, Qian Y, Weyn-Vanhentenryck SM, Zhang C.
Bioinformatics. 2017 Feb 15;33(4):566-567. doi: 10.1093/bioinformatics/btw653.

Nat Biotechnol. 2011 Jun 1;29(7):607-14. doi: 10.1038/nbt.1873.
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.
Zhang C, Darnell RB.

mCarts 1.2.0 – Hidden Markov model to predict Clustered RNA Motif sites

mCarts 1.2.0

:: DESCRIPTION

mCarts is a hidden Markov model (HMM)-based methods to predict clusters RNA motif sites.

::DEVELOPER

Zhang Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 mCarts

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Aug;41(14):6793-807. doi: 10.1093/nar/gkt421. Epub 2013 May 18.
Prediction of clustered RNA-binding protein motif sites in the mammalian genome.
Zhang C1, Lee KY, Swanson MS, Darnell RB.