Paper Info
Title
FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing.
Abstract
RNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs and the corresponding coding DNA sequences. Software tools successful for the search of genes in other organisms not always are able to correctly perform this task in plants organellar genomes. Moreover, the available software tools predicting RNA editing events utilise algorithms that do not account for events which may generate a novel start codon. We present Fedro, a Java software tool implementing a novel strategy to generate candidate Open Reading Frames (ORFs) resulting from Cytidine to Uridine (c→u) editing substitutions which occur in the mitochondrial genome (mtDNA) of a given input plant. The goal is to predict putative proteins of plants mitochondria that have not been yet annotated. In order to validate the generated ORFs, a screening is performed by checking for sequence similarity or presence in active transcripts of the same or similar organisms. We illustrate the functionalities of our framework on a model organism. The proposed tool may be used also on other organisms and genomes. Fedro is publicly available at http://math.unipa.it/rombo/FEDRO .
Year
DOI
Venue
2019
10.1186/s12859-019-2696-6
BMC Bioinformatics
Keywords
Field
DocType
RNA editing, Plants, ORFs generation
Genome,Start codon,Gene,Biology,Gene expression,RNA editing,DNA,DNA sequencing,Genetics,DNA microarray
Journal
Volume
Issue
ISSN
4
suppl
1471-2105
Citations 
PageRank 
References 
0
0.34
0
Authors
6
Name
Order
Citations
PageRank
Fabio Fassetti122322.68
Claudia Giallombardo201.01
Ofelia Leone301.35
Luigi Palopoli412617.24
Simona E. Rombo519222.21
Adolfo Saiardi601.01