Tag: piRNA

piRPred 1.0 – piwi interacting RNA (piRNA) Prediction

piRPred 1.0

:: DESCRIPTION

piRPred is a new modular and extensible machine learning method based on multiple kernels and a support vector machine (SVM) classifier for piRNA identification.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 piRPred

:: MORE INFORMATION

Citation

Towards a piRNA prediction using multiple kernel fusion and support vector machine.
Brayet J, Zehraoui F, Jeanson-Leh L, Israeli D, Tahi F.
Bioinformatics. 2014 Sep 1;30(17):i364-i370. doi: 10.1093/bioinformatics/btu441.

piRNA 3.6 / biRNA 3.6 – RNA Interaction Search Engine

piRNA 3.6 / biRNA 3.6

:: DESCRIPTION

piRNA is a parallel C++ package to compute joint and individual partition functions for two RNA sequences. From the partition functions, piRNA computes equilibrium concentrations of single and double joint species, ensemble energy, and melting temperatures.

biRNA is a fast open source tool based on a heuristic algorithm to compute RNA-RNA binding sites.

:DEVELOPER

Algorithmic Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 piRNA

:: MORE INFORMATION

Citation

Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen
A Partition Function Algorithm for Interacting Nucleic Acid Strands
Bioinformatics (2009) 25 (12): i365-i373.

piClust – Find piRNA Clusters and Transcripts from small RNA-seq data

piClust

:: DESCRIPTION

piClust uses a density based clustering approach without assumption of any parametric distribution to improve piRNA cluster identification.

::DEVELOPER

B&H Lab, Sun Kim group, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

piClust: a density based piRNA clustering algorithm.
Jung I, Park JC, Kim S.
Comput Biol Chem. 2014 Jun;50:60-7. doi: 10.1016/j.compbiolchem.2014.01.008.

piPipes 1.5.0 – piRNA Pipeline Collection

piPipes1.5.0

:: DESCRIPTION

piPipes is a coordinated set of pipelines to analyze piRNA (PIWI-interacting RNAs) and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq.

::DEVELOPER

ZLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • C++ Compiler

:: DOWNLOAD

 piPipes

:: MORE INFORMATION

Citation

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.
Han BW, Wang W, Zamore PD, Weng Z.
Bioinformatics. 2014 Oct 17. pii: btu647.

pirnaPre 1.0.0 – piRNA Targets on mRNAs in Mouse

pirnaPre 1.0.0

:: DESCRIPTION

pirnaPre is a SVM classifier based on a combination of Miwi CLIP-Seq derived features and position derived features to predict potential targets of piRNAs on mRNAs.

::DEVELOPER

pirnaPre team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pirnaPre

:: MORE INFORMATION

Citation

Computational identification of piRNA targets on mouse mRNAs.
Yuan J, Zhang P, Cui Y, Wang J, Skogerbø G, Huang DW, Chen R, He S.
Bioinformatics. 2015 Dec 16. pii: btv729.