Anouar Boucheham & Vivien Sommard

IBISC Lab

FEATURES

# 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:

Cross-Validation PredictionTraining & Prediction

# 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 ’U’ & tenth ’A’
• 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