RAST

[…] concisus whole genomes using a previously described method36. briefly, the 104 genomes from this study and an additional 9 c. concisus reference genomes were automatically annotated using the seed/rast system37,38 and a pangenome reference list of unique genes was assembled using blast with the following parameters: a sequence was considered to be an allelic variant of an existing gene […]

[…] for the plasmid) using bowtie 2 version 2.2.6 (34). sequence data were de novo assembled using spades version 3.8.0 (35), and functional annotations were obtained for contigs of interest using rast (36). regions of similarity between host and clone dna were identified using mauve (37). data analyses were performed in r, including packages rsamtools, gviz, ape, and genoplotr., raw sequence […]

[…] 7.5). the bb01 genome (1,271× coverage) had a g+c content of 51.8%, with 2,517,579 bp distributed among 84 contigs ranging in size from 1,006 bp to 197,455 bp. annotation was performed by the rast server (http://rast.nmpdr.org/) (5). the bb01 genome was predicted to have a total of 2,943 open reading frames (orfs) and 48 rna genes., to evaluate the subspecies status of bb01 strain, […]

[…] the blast tool to investigate the presence of several different r391 (ay090559) and sxt (ay055428) core scaffold genes (int, jef, tralekbva, setcd). the r997 sequence was then annotated using the rast server (rapid annotation using subsystem technology) and the basic local alignment search tool (blast) programme at ncbi31, 32. any gaps among the sequence were filled in by pcr-linkage […]

[…] whole genome assembly was performed with the gs de novo assembler using default parameters (microsynth). the fully assembled genome was annotated using rapid annotations using subsystems technology (rast) (aziz et al., 2008; overbeek et al., 2014; brettin et al., 2015) and the default setting options. additionally, genome annotation was verified and curated by blast analysis (altschul et al., […]