Open AccessReFernment: An R package for annotating RNA editing in plastid genomes
Author(s) -
Robison Tanner A.,
Wolf Paul G.
Publication year - 2019
Publication title -
applications in plant sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.64
H-Index - 23
ISSN - 2168-0450
DOI - 10.1002/aps3.1216
Subject(s) - biology , annotation , rna editing , genome , rna , plastid , computational biology , software , flagging , genetics , computer science , gene , chloroplast , programming language , history , archaeology
Premise of the Study In the absence of cDNA , the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts. Methods and Results We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors. Conclusions Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of plastome sequences for taxa with high levels of RNA editing.