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[…] was selected for codon usage analysis. The 54 single-copy panorthologs from the reduced set of taxa were aligned with Probcons () and trimmed with BMGE () with default parameters. A tree was inferred using RAxML with the PROTGAMMALG model and 100 bootstrap pseudoreplicates. The Bifidobacterium data set was treated similarly: OrthoMcl was first used to detect 400 single-copy panorthologs, which were then aligned with Mafft-linsi (), trimmed for positions with over 50% gaps, and concatenated with local perl scripts. A tree was then reconstructed with RAxML as before., Genome statistics, including GC content, GC3s and Nc, and correspondence analyses were calculated with the aid of the software CodonW (). The Nc values were calculated based on the GC3s values by the method defined by Wright, as Ncexpect = 2 + GC3s + 29/(GC3s + (1−GC3s)2) (; ). The codon usage index (CAI) was calculated by CAI and cusp function from EMBOSS package (). The relative synonymous codon usage (RSCU) values were calculated using the program GCUA (General Codon Usage Analysis) (). The strength of selected codon usage bias was estimated from the S index, which is used as a proxy for translational selection on individual genomes (, ). The number of tRNA genes and the inference of anti-codons were made with the aid of tRNAscan-SE 1.3.1 (). Other statistics, including length of CDS and nucleotide position within the genome, were calculated from Genbank or annotation files using Perl and R scripts., The genes in each data set were categorized into highly expressed and all genes (). The highly expressed genes were defined as in (), and included genes for translation elongation factor Tu, Ts and G, and 37 large ribosomal proteins, incl […]

Pipeline specifications

Software tools CodonW, EMBOSS, GCUA