PT  - JOURNAL ARTICLE
AU  - Atul Kakrana
AU  - Pingchuan Li
AU  - Parth Patel
AU  - Reza Hammond
AU  - Deepti Anand
AU  - Sandra M. Mathioni
AU  - Blake C. Meyers
TI  - <em>PHASIS</em>: A computational suite for <em>de novo</em> discovery and characterization of phased, siRNA-generating loci and their miRNA triggers
AID  - 10.1101/158832
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 158832
4099  - http://biorxiv.org/content/early/2017/07/03/158832.short
4100  - http://biorxiv.org/content/early/2017/07/03/158832.full
AB  - 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 “PHAS” 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.