Computational protocol: Splicing Variants of SERPINA1 Gene in Ovine Milk: Characterization of cDNA and Identification of Polymorphisms

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Protocol publication

[…] Whole mammalian genome scanning was done to identify the homologous regions of the full length sheep SERPINA1 cDNA and gene using Basic Local Alignment Search Tool ( Sequence data were edited, translated and aligned using the free software Bioalign 4.0.6 ( The open reading frame (ORF) of the full-length AAT cDNA was determined by ORF Finder at NCBI ( identify SNPs with potential impact on splicing of SERPINA1 gene, mutant and wild sequences were analyzed with the Human Splicing Finder software (, which includes several matrices to analyze splice sites and splicing silencers and enhancers.To determine the potential deleterious effect of amino acid changes on protein function we used the SIFT ( software. This software uses the protein sequence similarity of different species and the characteristics of amino acids (structure, polar/no polar, basic/acid) to calculate the probability of a deleterious effect of specific amino acid variants. Scores lower than 0.05 suggest a potential not tolerated amino acid substitution and a potential influence on protein function.To search for homology of the predicted protein sequence with other species the BLASTP software was used ( We aligned the AAT protein sequences of different organisms with MEGA5 software ( [] to examine the evolutionary conservation of RCL motifs. […]

Pipeline specifications

Software tools BLASTN, BioLign, Open Reading Frame Finder, HSF, SIFT, BLASTP, MEGA
Applications WGS analysis, Nucleotide sequence alignment
Organisms Ovis aries, Homo sapiens, Bos taurus