EvryRNA : IpiRId

Integrative piRNA Identification

Anouar Boucheham & Vivien Sommard



# IpiRId is an instance of IncRId tool, specific for predicting piRNAs from different sources of data:

  • positions on the genome
  • reference genome
  • transposons
  • chIP-Seq data (positions of histone methylations: H3K9me3 & H3K27me3)
  • positions of Centromeres and Telomeres

# Positions of positive and negative sequences must be aligned onto human hg38, Mouse mm10 and fly dm6 reference genomes, in order to have more accurate predictions

# IpiRId allows three execution mode:

# Available species: Homo sapiens, Mus musculus and Drosophila melanogaster.

# IpiRId can be performed using one or many kernels corresponding to the studied piRNA's features.

# Available kernels list:

  • First ā€™Uā€™ & tenth ā€™Aā€™
  • K-mer frequencies
  • K-mer positions
  • Transposons binding
  • Centromeres/Telomeres
  • Histones methylation
  • Clusters
  • A-Myb
  • G-Quadruplex
  • CpG islands
  • LINEs, SINEs and LTRs
  • Inverted repeats
How to cite IpiRId:
  • A. Boucheham, V. Sommard, F. Zehraoui, A. Boualem, M. Batouche, A. Bendahmane, D. Israeli and F. Tahi. IpiRId: Integrative approach for piRNA prediction using genomic and epigenomic data. PloS one 2017; 12(6), e0179787. doi:10.1371/journal.pone.0179787
For any questions, comments or suggestions about IpiRId, please feel free to contact: anouarboucheham@gmail.com and fariza.tahi@ibisc.univ-evry.fr