Computational protocol: Release of Nonstop Ribosomes Is Essential

Similar protocols

Protocol publication

[…] The protein sequence of CC1214 was used in a tblastn search () of the June 2014 NCBI database of representative microbial genomes. An E value cutoff of 10−7 and a molecular-mass cutoff of 20 kDa were used to identify homologs. In cases where a homolog was identified for a given phylum, that homolog was then used in a tblastn search of the remaining representative genomes in that phylum. If a homolog was not found, tblastn searches were performed with homologs from closely related phyla. A tree of Alphaproteobacteria species was constructed by collecting 16S rRNA gene sequences from PATRIC () and aligning them with BLAST. The tree was viewed and colored using Fig tree software (version 1.4.2 [http://tree.bio.ed.ac.uk/software/figtree/]). […]

Pipeline specifications

Software tools TBLASTN, FigTree
Databases PATRIC
Applications Phylogenetics, Amino acid sequence alignment
Organisms Caulobacter vibrioides, Escherichia coli