September 22, 2019  |  

PHASIS: A computational suite for de novo discovery and characterization of phased, siRNA-generating loci and their miRNA triggers

Authors: Kakrana, Atul and Li, Pingchuan and Patel, Parth and Hammond, Reza and Anand, Deepti and Mathioni, Sandra and Meyers, Blake

Phased, secondary siRNAs (phasiRNAs) are found widely in plants, from protein-coding transcripts and long, non-coding RNAs; animal piRNAs are also phased. Integrated methods characterizing textquotedblleftPHAStextquotedblright loci are unavailable, and existing methods are quite limited and inefficient in handling large volumes of sequencing data. The PHASIS suite described here provides complete tools for the computational characterization of PHAS loci, with an emphasis on plants, in which these loci are numerous. Benchmarked comparisons demonstrate that PHASIS is sensitive, highly scalable and fast. Importantly, PHASIS eliminates the requirement of a sequenced genome and PARE/degradome data for discovery of phasiRNAs and their miRNA triggers.

Journal: BioRxiv
DOI: 10.1101/158832
Year: 2017

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