Computational protocol: Identification and caste-dependent expression patterns of DNA methylation associated genes in Bombus terrestris

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Protocol publication

[…] Nucleotide sequences of genes were obtained from the National Center for Biotechnology Information with blast tool. Putative ORFs and amino acid sequences of DNA methylation-associated genes in B. terrestris were predicted using DNAMAN software. Protein properties were analyzed with EXPASy server, and protein domains were predicted with SMART software. Sequences used in phylogenetic analysis were downloaded from the National Center for Biotechnology Information gene database (http://www.ncbi.nlm.nih.gov). DNA methylation-associated genes of B. terrestris and other selected insects were subjected to multiple sequence alignments using Clustal W program and edited with GeneDoc software (Supplementary Figs –). The phylogenetic trees were constructed using a Maximum Likelihood method with a Poisson model and 1000 Bootstrap replications of MEGA5.0 software. […]

Pipeline specifications

Software tools DNAMAN, Clustal W, MEGA
Databases ExPASy
Application Phylogenetics
Organisms Bombus terrestris