Computational protocol: Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals

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Protocol publication

[…] We retrieved gene contents within SD regions based on genome annotation files downloaded from NCBI (e.g., ftp://ftp.ncbi.nih.gov/genomes/Sus_scrofa/mapview/seq_gene.md.gz). Bioconductor (http://www.bioconductor.org/) was used to perform Gene Ontology (GO) analyses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted with DAVID (http://david.abcc.ncifcrf.gov/). Since only a limited number of genes in the livestock genomes have been annotated, we firstly converted the gene IDs of investigated livestock species to orthologous human Ensembl gene IDs by BioMart (http://www.biomart.org/), then carried out the GO and KEGG pathway analyses. We also analyzed orthologous protein-coding genes within SD regions among domestic animals based on OrthoDB release 7 (http://cegg.unige.ch/orthodb7). The phylogenetic trees were drawn using Clustal X (http://www.clustal.org/clustal2/) and Tree View (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html). […]

Pipeline specifications

Software tools DAVID, BioMart, Clustal W, TreeViewX
Databases OrthoDB KEGG PATHWAY
Applications Genome annotation, Phylogenetics
Organisms Oryctolagus cuniculus, Gallus gallus, Ovis aries, Capra hircus, Equus caballus, Bos taurus, Sus scrofa
Chemicals Uridine Diphosphate