Paper Info
Title
SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs.
Abstract
High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline optimized for rRNA- and tRNA-derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users’ input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.
Year
DOI
Venue
2018
10.1016/j.gpb.2018.04.004
Genomics, Proteomics & Bioinformatics
Keywords
Field
DocType
Small RNA,RNA-seq data analysis,tsRNA,rsRNA,Annotation pipeline
Small RNA,Biology,Ribosomal RNA,Profiling (computer programming),Small nucleolar RNA,Transfer RNA,microRNA,RNA modification,Genetics
Journal
Volume
Issue
ISSN
16
2
1672-0229
Citations 
PageRank 
References 
0
0.34
8
Authors
5
Name
Order
Citations
PageRank
Junchao Shi100.68
Eun-A Ko200.68
Kenton M. Sanders321.04
Qi Chen401.01
Tong Zhou544876.83