RAST

[…] draft genome completeness and contamination was assessed using checkm (). the final draft genome was annotated using the ncbi prokaryotic genome annotation pipeline (pgap) () and reviewed using rast v2.0 ()., this resulted in a 3.47-mbp draft genome estimated to be 93.9% complete with 1.79% potential contamination, comprising 5 scaffolds with a gc content of 36%, 3,354 coding sequences, 34 […]

[…] and gca_000686085.1 (marinobacter hl-58). the genomes were annotated integrating information from the following pipelines: 1) the doe-jgi microbial genome annotation pipeline, blastkoala, and the rast server, as previously described. annotations are available on github (see below) and through img (http://img.jgi.doe.gov). the total number of protein encoding genes identified for halomonas […]

[…] annotation were conducted using glimmer version 3.02 (), prodigal version 1.20 (), genemarks version 4.08 (), and protein blast () and confirmed by the rapid annotations using subsystems technology (rast) version 2.0 server (). trnas were predicted using trnascan-se version 2.0 (), and the nucleotide homology of pvco-5 was determined using emboss stretcher ()., the genome of pvco-5 comprised […]

[…] on a miseq sequencer (illumina, inc., san diego, ca, usa) using the paired-end strategy. raw reads were assembled with a5-miseq software (). genome and subsystem-based annotations were performed by rapid annotation using subsystem technology (rast) (, ). trna gene detection was performed using the trnascan-se 2.0 tool (), whereas rrna genes were predicted using rnammer (). plasmid presence […]

[…] contig was 455,093 bp, and the shortest contig was 2,842 bp. the assembly produced an estimated genome of approximately 2.36 mb, with 40.7% g+c content. an initial gene inspection was made with the rapid annotation using subsystem technology (rast) pipeline (). finally, automatic gene prediction and annotation were performed using the ncbi prokaryotic genome annotation pipeline […]

[…] ordering and manual curation was conducted using geneious mapper with high sensitivity and up to five times iteration in geneious 10 workbench, following automated annotation of draft genomes in rast. genomes are deposited in genbank under cp025423-cp025424 for horse_pl chromosome and plasmid, and pjpx00000000 for 10652_placenta; pjpy00000000 for 9945_foetus, pjpz00000000 for 8882_foetus […]

[…] assembled de novo using spades algorithm (spades version 3.7.1) for illumina-derived reads and then manually curated to close the gaps. putative open reading frames (orfs) were identified by rast version 2.0 and manually curated when necessary. blastp analyses of the putative orfs against the ncbi non-redundant proteins (nr) database, pfam, and interpro scan were used to assess […]

[…] (7 genes for 5s, 6 for 16s, and 6 for 23s), 60 trnas, and 4 noncoding rnas. a total of 108 pseudogenes were predicted. functional annotation using the rapid annotations using subsystems technology (rast) server () revealed that 75 of the genes were associated with virulence, disease, and defense, 140 genes with rna metabolism, 196 genes with carbohydrate metabolism, and 259 genes […]

[…] of each contig (unitig_0: 4,903,991; unitig_1: 123,705; unitig_2: 118,720; unitig_3: 30,364); the final sizes are reported in table .table 3, the complete genome sequence was annotated with the rast server [] which predicted 5028 coding sequences and 110 rnas., a summary of the genome of e. coli 1094 is included in table . the genome statistics are provided in table . three putative […]

[…] (). the draft genome sequence of p. hydrolytica s66t is available from genbank, acc. no. lsne00000000 (). the results presented here are based on protein predictions and locus tags generated by rast (), and are accessible on the rast guest account under genome id 89404.4 (using login and password ‘guest’). for convenience the rast generated locus tag prefix (fig|89404.4.peg.) was renamed […]