Lee et al. BMC Genomics 2011, 12:197 http://www.biomedcentral.com/1471-2164/12/197 Page 5 of 6 Table 1 Differences in the size of predicted translation products between the Serva ILTV strain and the concatenated ILTV reference sequence ORF Concatenated ILTV reference sequencea Serva ILTV sequencea Nucleotide start Nucleotide end ORF length (aa) Nucleotide start Nucleotide end ORF length(aa) UL56 7316 8170 855 (284) 7062 7886 825 (274) ORF F 8301 10559 2259 (752) 8017 10257 2241 (746) UL54 10784 12046 1263 (420) 10646 12280 1635 (544) UL25 35392 37110 1719 (572) 35149 36927 1779 (592) UL29 44095 47094 3000 (999) 43851 47381 3531 (1176) UL30 47271 50294 3024 (1007) 47558 50836 3279 (1092) UL31 50464 51483 1020 (339) 50826 51770 945 (314) UL36 54914 62584 7671 (2556) 55201 63555 8355 (2784) UL37 63209 65881 2673 (890) 63694 66762 3069 (1022) UL38 66045 67283 1239 (412) 66926 68374 1449 (482) UL42 72398 73696 1299 (432) 73276 74586 1311 (436) ICP4 114497 118888 4392 (1463) 115301 119749 4449 (1482) 142837 147228 4392 (1463) 146812 151260 4449 (1482) a Bold texts indicate large differences (>50 amino acids) in the size of predicted gene products the terminal repeat region (identical to the internal repeat region), which was excluded from the analysis. ILTV DNA sequence analysis The software package Geneious [25] was used to manu- ally curate the alignments of the contigs and to produce a consensus sequence with reference to the original mapped reads. Any sequence gaps or ambiguous regions of sequence were amplified and sequenced by Sanger sequencing methods using BDT version 3.1 (Applied Biosystems). Nucleotide and amino acid sequence align- ments were performed using ClustalW version 2.0 [26], ORFs were then annotated using the Geneious software package. Open reading frames containing more than 50 amino acids were predicted using the ORF finder func- tion of Geneious, based on the complete concatenated ILTV genomic sequence. Nucleotide sequence accession numbers The complete genome sequence of Serva ILTV has been deposited in the NCBI GenBank database under accession HQ_630064. The concatenated ILTV geno- mic sequence is available in the GenBank database under accession NC_006623. Nucleotide sequences for psittacid herpesvirus-1 (PsHV1), equid herpesvirus-1 (EHV1) and herpes simplex virus-1 (HSV1) were also utilized in this study. The translated amino acid sequences for the UL29 genes of these viruses are available in the GenBank database under accessions NP_944402, YP_053076 and NP_044631, respectively. The translated amino acid sequences for the UL36 genes of these viruses are available in the GenBank database under accessions NP_944409, YP_053069 and ABI63498, respectively. Additional material Additional file 1: Summary of nucleotide differences. Nucleotide differences detected between the concatenated ILTV reference sequence and the Serva ILTV sequence after whole genome alignment. Additional file 2: Summary of all amino acid differences. Amino acid differences detected between the predicted translation products of the concatenated ILTV reference sequence and the Serva ILTV sequence. Acknowledgements The Rural Industries Research and Development Corporation, Australia, funded this study. JMD is supported by a fellowship from the Australian Research Council. NICTA is funded by the Australian Government as represented by the Department of Broadband, Communications and the Digital Economy and the Australian Research Council through the ICT Centre of Excellence program. The authors thank Kelly Ewen-White (Lifetech) for her expert advice and assistance. Author details 1Asia-Pacific Centre for Animal Health, School of Veterinary Science, The University of Melbourne, Parkville, Victoria, 3010, Australia. 2Applied Biosystems, Australia. 3National ICT Australia, Department of Electrical and Electronic Engineering, The University of Melbourne, Victoria, 3010 Australia. Authors’ contributions S-WL carried out the sequencing studies, sequence analyses, sequence alignments and drafted the manuscript. NPF performed preparation of viral DNA. IP performed sequencing. JFM performed sequence analyses. CAH performed preparation of viral DNA, participated in sequence analyses and helped to draft the manuscript. JMD, PFM, GFB and AHN conceived of the study, designed and coordinated the study, participated in preparation of viral DNA, sequencing studies, sequence analyses, and helped to draft the manuscript. All authors read and approved the final manuscript. Received: 1 December 2010 Accepted: 19 April 2011 Published: 19 April 2011 References 1. Bagust TJ, Jones RC, Guy JS: Avian infectious laryngotracheitis. Rev Sci Tech 2000, 19(2):483-492. 2. Roizmann B, Desrosiers RC, Fleckenstein B, Lopez C, Minson AC, Studdert MJ: The family Herpesviridae: an update. The Herpesvirus Study