RAST

[…] ntig 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 and […]

[…] equently 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 their puta […]

[…] s (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 with metabolism […]

[…] tamination), based on operational standards for SAGs (), and contains 1,646 protein-coding genes plus 40 RNA-coding genes annotated with PGAP () and the Rapid Annotations using Subsystems Technology (RAST) server (). The SAG contained a 16S rRNA gene sequence with 99% identity to environmental SA1 sequences from DHABs but only 93% identity to Methanonatronarchaeia representatives (). Also, all thr […]

[…] The sequence of the Stx converting phage was extracted from the complete genome by using the PHASTER (http://phaster.ca/), the genome of Stx converting phage was reannotated using the RAST server (http://rast.nmpdr.org/), and then manually verified and corrected. Functional annotation of selected CDSs was performed based on the results of homology searches against the public nonred […]

[…] ry phylogenetic assignment of obtained composite genomes were assessed with CheckM. For each composite genome, gene search and annotation were performed for all contigs longer than 2000 bp, using the RAST server, followed by manual correction by searching the National Center for Biotechnology Information (NCBI) databases. The 16S ribosomal RNA genes were found in contigs by CheckM. The search for […]