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Protocol publication

[…] drophobic amino acids of cSox2 using the Eisenberg’s method was used (), which shows that the cSox2 protein has more hydrophobic amino acids at its N-terminal tail than at its C-terminal tail. The expected isoelectric point (pI) was found to be 10.11. The N-terminal of the sequence was considered M (Met). The chemical composition of the predicted cSox2 protein is illustrated in and . As shown in , the cSox2 protein is rich in Serine (S) residue, which constitutes 12.5% of the total amino acids. It has been shown that this amino acid is rich in transcription factors., When the predicted sequence of amino acids of cSox2 was contrasted with the top similar sequences from six species using the BLASTP algorithm on the NCBI Blast server (http://blast.ncbi.nlm.nih.gov/Blast.cgi), the relative percentage identities were ranging from 99% to 93%: 99% for Homo sapiens, Mus musculus, Bos taurus, and Vicugna pacos; 98% for Sus scrofa; and 93% for Camelus ferus (). The multiple alignments of amino acid sequences used for this analysis are presented in ., The amino acid sequence of cSox2 was aligned with that of six mammalian species by ClustalW alignment using Geneious 7.1.7 software. In general, the amino acid alignment of the cSox2 and six mammalian species has shown that the N-terminus is more conserved than the C-terminus. A conserved sequence of about 75 residues (red line) revealed the HMG-box domain ()., In order to identify the ordered “globular” and disordered regions of the cSox2 protein, we used the GlobPlot 2.3 server at the globplot.embl.de website. The Russell/Linding set was chosen in which the structures of α-helices and β-sheets are assigned as globular regions (GlobDoms), whereas the structures of random coils and turns are as disordered regions (Disorder). This method can predict a novel propensity based on the disorder predicti […]

Pipeline specifications

Software tools BLASTP, Clustal W, Geneious
Organisms Homo sapiens, Camelus dromedarius, Mus musculus, Bos taurus, Vicugna pacos, Sus scrofa, Camelus ferus
Chemicals Amino Acids