Computational protocol: Identification and Functional Analysis of Three Isoforms of Bovine BST-2

Similar protocols

Protocol publication

[…] Three isoforms of bBST2 were mapped into the bovine genome (UMD 3.1 assembly) using the BLAT program . Multiple amino acid sequence alignment was performed using L-INS-i in MAFFT and modified it manually. Based on the amino acid alignment, nucleotides from each isoform were aligned using TranslatorX . The amino acid substitution model of JTT with gamma-distributed rate variation (+Γ, α = 0.591) was selected using the Akaike information criterion implemented in PROTTEST 3 . A phylogenetic tree was constructed using the maximum-likelihood method in RAxML v7.2.6 with robustness evaluated by rapid bootstrapping (1,000 times). […]

Pipeline specifications

Software tools BLAT, MAFFT, TranslatorX, ProtTest, RAxML
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Bos taurus, Homo sapiens, Sus scrofa, Mus musculus, Ovis aries
Diseases HIV Infections, Enzootic Bovine Leukosis