Computational protocol: Chimeric Sex-Determining Chromosomal Regions and Dysregulation of Cell-Type Identity in a Sterile Zygosaccharomyces Allodiploid Yeast

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Protocol publication

[…] Sequences were assembled and edited using DNAStar Software (DNASTAR, Inc. Madison, Wisconsin USA). Multiple nucleotide and amino acid sequence alignments were performed using Clustal W2 []. Searches for nucleotide and protein sequence homologs were carried out in the GenBank database with Blastn and Blastp algorithms, respectively []. Phylogenetic analysis was conducted on aa sequences using MEGA6 []. The phylogenetic relationship was inferred using the neighbour-joining (NJ) method. Support percentages for the nodes of NJ-trees were computed using bootstrapping analysis with 1,000 replications and were shown next to the branches when ≥ 60%. For domain identification, Pfam-searches [] were run on http://pfam.sanger.ac.uk/. Structure predictions were obtained with Jpred3 [] and validated according to Martin et al. []. Sequences were submitted to the EMBL/GenBank databases under the accession numbers from KT598024 to KT598027 and from KT694298 to KT6942302. […]

Pipeline specifications

Software tools Clustal W, BLASTN, BLASTP, MEGA, JPred
Databases Pfam
Application Phylogenetics
Organisms Saccharomyces cerevisiae, Zygosaccharomyces rouxii