Computational protocol: Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

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Protocol publication

[…] In GenBank, there are whole-genome RefSeqs for six Orbivirus species: Bluetongue virus (BTV), African horse sickness virus (AHSV), Peruvian horse sickness virus (PHSV), Yunnan orbivirus (YUOV), Palyam virus (PALV) and Saint Croix river virus (SCRV). All six genomes comprise 10 segments. The segments homologous to BTV segment 9 (encoding VP6) were identified by finding the best blastp-match, among the 10 BTV translated segments, for the longest ORF in each of the 50 non-BTV segments. The identifications were verified, where possible, by information in the GenBank-file headers and in the literature (AHSV []; YUOV []; PALV []; SCRV []).As of 11 May 2007, there were 1273 Orbivirus sequences in GenBank (i.e. including partial sequences), however most of these are not segment 9. Incidently, none of these sequences has more than one CDS annotated. Segment 9 sequences were extracted (a) using the GenBank-file DEFINITION headers, and (b) by finding the best blastp-match for the longest ORF in each sequence among the 10 BTV translated segments. These were supplemented with all GenBank (16 Mar 2008) tblastn matches to the ORFX peptide sequences from the six RefSeqs (providing one additional recent sequence). After removing duplicate sequences, the following segment 9 sequences were found: (1) the 6 RefSeqs for BTV, AHSV, PHSV, YUOV, PALV and SCRV (all complete); (2) 47 other BTV sequences (mostly complete VP6 CDS; all cover ORFX completely; ~34 contain the full 5' UTR); (3) 2 other AHSV sequences (full genome); and (4) 10 PALV partial sequences (183 nt, completely contained in the ORFX region).The GenBank accession numbers are as follows: BTV – NC_006008, A22393, AF403418, AF403419, AF403420, AF403421, AF403423, AY124373, AY493691, D10905, DQ289041, DQ289042, DQ289043, DQ289044, DQ289045, DQ289046, DQ289047, DQ289048, DQ289050, DQ825668, DQ825669, DQ825671, DQ832170, L08668, L08669, L08670, L08671, L08672, U55778, U55779, U55780, U55781, U55782, U55784, U55785, U55786, U55787, U55788, U55790, U55792, U55793, U55794, U55795, U55796, U55797, U55799, U55800, U55801; AHSV – NC_006019, U19881, AM883170; PHSV – NC_007753; YUOV – NC_007664; PALV – NC_005992, AB034675, AB034676, AB034677, AB034678, AB034679, AB034680, AB034681, AB034682, AB034683, AB034684; SCRV – NC_006005. […]

Pipeline specifications

Software tools BLASTP, TBLASTN
Application Amino acid sequence alignment
Organisms Bluetongue virus, African horse sickness virus, St Croix River virus
Diseases HIV Infections