Computational protocol: Sequence analysis of the 5′ third of glycoprotein C gene of SouthAmerican bovine herpesviruses 1 and 5

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Protocol publication

[…] The PCR amplicons were purified using an Illustra™ GFX™ PCR DNA and Gel Band Purification Kit (GE Healthcare, UK), according to the manufacturer's instructions. Sequencing reactions were performed twice and in both directions in an automatic sequencer ABI-PRISM 3100 Genetic Analyzer (Applied Biosystems, USA). DNA amplicons (30-60 ng) and 4.5 pmol of forward or reverse specific 5′ gC primers of each type (described above) were used for sequencing (for more sequencing details see (Ref. )).The quality of nucleotide sequences and overlapping fragments of each sequence were assembled by the Staden Package, which was submitted for comparison with reference sequences of BoHV-1.1 (strain Cooper; GenBank no. AJ004801) and BoHV-5 (SV 507/99; GenBank no. AY261359) complete genomes, using the National Center for Biotechnology Information (NCBI) database and BLAST software (http://www.ncbi.nlm.nih.gov/BLAST/). Based on nucleotide sequences, amino sequences were translated in reading frame 1 on the direct strand by Sequence Manipulation Suite software version 2 (http://www.bioinformatics.org/sms2/) and evaluated for homology comparison by protein BLAST. The nucleotide and deduced amino acid sequences of each isolate, and gC of reference sequences (GenBank ID AJ004801 and AY261359) were aligned and edited with the BioEdit Sequence Alignment Editor software suite, version 7.0.5.3 (USA), using ClustalW software (Ireland). The identity matrix was also obtained using BioEdit software (,). […]

Pipeline specifications

Software tools DELTA-BLAST, BioEdit, Clustal W
Application Amino acid sequence alignment
Organisms Bos taurus, Bovine alphaherpesvirus 1, Bovine alphaherpesvirus 5
Diseases Porokeratosis
Chemicals Amino Acids, Nucleotides