miRNAFold – Ab initio miRNA Precursor Search in Genomes

miRNAFold

:: DESCRIPTION

miRNAFold is a fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRNAFold: a web server for fast miRNA precursor prediction in genomes.
Tav C, Tempel S, Poligny L, Tahi F.
Nucleic Acids Res. 2016 May 29. pii: gkw459.

Nucleic Acids Res. 2012 Jun;40(11):e80. doi: 10.1093/nar/gks146. Epub 2012 Feb 22.
A fast ab-initio method for predicting miRNA precursors in genomes.
Tempel S1, Tahi F.

iMcRNA / miRNA-dis – microRNA Precursor Identification based on Distance Structure Status Pairs

 iMcRNA / miRNA-dis

:: DESCRIPTION

The web-server iMcRNA was developed for identifying the real microRNA precursors and false microRNA precursors.

miRNA-dis: microRNA precursor identification based on distance structure status pairs

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Identification of real microRNA precursors with a pseudo structure status composition approach.
Liu B, Fang L, Liu F, Wang X, Chen J, Chou KC.
PLoS One. 2015 Mar 30;10(3):e0121501. doi: 10.1371/journal.pone.0121501.

Mol Biosyst. 2015 Apr;11(4):1194-204. doi: 10.1039/c5mb00050e.
miRNA-dis: microRNA precursor identification based on distance structure status pairs.
Liu B1, Fang L, Chen J, Liu F, Wang X.

miRNA-deKmer – Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy

miRNA-deKmer

:: DESCRIPTION

miRNA-deKmer is a web server of identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.
Liu B, Fang L, Wang S, Wang X, Li H, Chou KC.
J Theor Biol. 2015 Nov 21;385:153-9. doi: 10.1016/j.jtbi.2015.08.025.

ViralMir – Identify the microRNA Precursor in Virus

ViralMir

:: DESCRIPTION

ViralMir is the first public resource dedicated to identify the microRNA precursor in virus.

::DEVELOPER

CSB Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors.
Huang KY, Lee TY, Teng YC, Chang TH.
BMC Bioinformatics. 2015;16 Suppl 1:S9. doi: 10.1186/1471-2105-16-S1-S9.

NeuroPID 201503 – Neuropeptide-Precursor Identifier

NeuroPID 201503

:: DESCRIPTION

NeuroPID is a prediction tool for Neuropeptide Precursors (NPPs) and Neuromodulators

::DEVELOPER

The Sudarsky Center for Computational Biology – The Hebrew University of Jerusalem

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NeuroPID: a classifier of neuropeptide precursors.
Karsenty S, Rappoport N, Ofer D, Zair A, Linial M.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W182-6. doi: 10.1093/nar/gku363.

mirnaDetect – Predict possible microRNA Precursors within Genome data

mirnaDetect

:: DESCRIPTION

A java based mining tool mirnaDetect is developed for detect potential pre-miRNAs from the genome-scale data. This program is based both on search and machine learning algorithms.

::DEVELOPER

Leyi Wei, Dr. Quan Zou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 mirnaDetect

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov 8.
Improved and Promising Identification of Human MicroRNAs by Incorporating a High-quality Negative Set.
Wei L, Liao M, Gao Y, Ji R, He Z, Zou Q.

iMiRNA-PseDPC – microRNA Precursor Identification with a Pseudo Distance-pair Composition Approach

iMiRNA-PseDPC

:: DESCRIPTION

The web-server iMiRNA-PseDPC was developed for identifying the real microRNA precursors and false microRNA precursors.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2015 Feb 3:1-28. [Epub ahead of print]
iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach.
Liu B1, Fang L, Liu F, Wang X, Chou KC.

PeptideReranking – Peptide Re-ranking with Protein-peptide Correspondence and Precursor Peak Intensity Information

PeptideReranking

:: DESCRIPTION

PeptideReranking includes three peptide reranking methods: PPMRanker, PPIRanker, and MIRanker. PPMRanker only uses Protein-Peptide Map (PPM) information from the protein database, PPIRanker only uses Precursor Peak Intensity (PPI) information, and MIRanker employs both PPM information and PPI information.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PeptideReranking

:: MORE INFORMATION

Citation:

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1212-9. doi: 10.1109/TCBB.2012.29.
Peptide reranking with protein-peptide correspondence and precursor peak intensity information.
Yang C1, He Z, Yang C, Yu W.

PITUFO – Find minimal sets of Precursors of Target Compounds in a Metabolic Network

PITUFO

:: DESCRIPTION

PITUFO is a java software to find minimal sets of precursors of target compounds in a metabolic network.

::DEVELOPER

Ludovic Cottret

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Java

:: DOWNLOAD

 PITUFO

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2010 Sep 2;6(9). pii: e1000904. doi: 10.1371/journal.pcbi.1000904.
Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.
Cottret L, Milreu PV, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot MF.