Pipeline publication

[…] ing conditions: initial bacterial lysis/denaturation 2 min at 94 °C, 30 cycles of 18 s at 94 °C, 30 s at 50 °C and 3 min at 72 °C, and a final extension of 5 min at 72 °C., PCR amplicons were sequenced using either the M13F primer used in the colony screening or both Mt_F and Mt_R primers for species identification. Further sequencing of full-length genome clones was performed by primer walking. Sequencing was carried out using BigDye Terminator v3.1 (Applied Biosystems) according to the manufacturer’s instructions. Sequences were read by Edinburgh Genomics. Sequences, with vector nucleotides removed, were submitted for analysis using the NCBI (National Center for Biotechnology Information) Basic Local Alignment Search Tool for nucleotide or translated sequence homology (blastn or blastx)., Sequence analysis and assembly was performed using sse v1.1 (). Protein coding sequences in complete genomes, identified using either sse v1.1 software or NCBI ORF Finder, were submitted for analysis using NCBI protein blast. Phylogenetic trees were reconstructed using maximum-likelihood methods as implemented in the mega6 software package ()., This work was funded by Biotechnology and Biological Sciences Research Council Institute Strategic Programme Grant funding to The Roslin Institute., One supplementary table is available with the online version of this paper.] […]

Pipeline specifications

Software tools BLASTN, BLASTX, MEGA
Organisms Mus musculus, Homo sapiens
Diseases Infection