Similar protocols

Pipeline publication

[…] Z 2.0 program can link the allele designations within the PubMLST database and draw an MSTree (). The MSTree was calculated by Prim’s algorithm and was incorporated with the eBURST algorithm to obtain a comprehensive and precise graphical result. The graphical results included different types of lines were used to illustrate the number of shared alleles, and the length of branches reflect the distance between different types. Further bioinformatics analysis, such as identification of genomic islands, insertion elements (IS), prophage sequences, clustered regularly interspaced short palindromic repeat (CRISPR) sequences and secondary metabolite gene clusters, were predicted by application of IslandViewer 3, ISfinder 1.0, PHASTER 2016, CRISPRFinder 1.0 and antiSMASH 4.0.0 tools with default parameters, respectively (, , , , ., The draft genome sequence of A. pittii TCM178 consisted of 43 contigs which comprised 3,789,564 bases, and PGAP server predicted a total of 3,501 protein-coding sequences. The overall G+C content of this strain amounted to 37.60%. In total, 63 tRNA genes and 3 rRNA operons were identified, respectively (). The distribution of genes into COGs functional categories is summarised in . We also identified the aminoglycoside resistance genes strA, strB and aph(3’)-VIa, beta-lactam resistance genes bla ADC-25, bla OXA-72 and bla OXA-213-like, macrolide resistance genes msr(E) and mph(E), and tetracycline re […]

Pipeline specifications

Software tools IslandViewer, PHASTER, CRISPRFinder
Databases ISfinder