EDGAR 2.0: an enhanced software platform for comparative gene content analyses

“…This pipeline uses Prodigal [26], RNAMMER [27] and ARAGORN [28] for the prediction of coding sequences, rRNAs, and tRNAs. Functional annotation is realized by a comparison of predicted coding sequences against a database of conserved orthologous groups of the genus Xanthomonas identified by the EDGAR software [29]. Genes that could not be annotated by this approach were compared to a collection of sequence databases comprising Swissprot, Refseq, and Pfam-A [30–32].…”

“…Comparative genome analysis was performed using EDGAR 2.0 [29]. The platform employs a bit score related cutoff value, which is generated based on BLAST score ratio values (SRVs) to identify orthologous genes.…”

“…1, b) [102]. A new version of EDGAR was published recently [103]. The main focus of the analysis of Xanthomonas genomes is usually on virulence factors [66].…”

“…It is particularly useful for RNA-Seq experiments. (b) Comparative genomics is facilitated by EDGAR software [102,103]. Despite being a stand-alone application, it is able to communicate with the well-established genome annotation software GenDB (c) [77], which can be complemented with SAMS for the analysis of shorter DNA sequence data [269].…”