Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 53. de Boer JG, Yazawa R, Davidson WS, Koop BF: Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids.BMC Genomics 2007, 8:422. 54. Thomson JD, Higgins DG, Gibson TJ: ClustalW: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice.Nucleic Acids Res 1994, 22:4673-4680. 55. TMHMM Server v. 2.0. Internet 2009 [http://www.cbs.dtu.dk/services/ TMHMM/]. 56. Sonnhammer EL, von Heijne G, Krogh A: A hidden Markov model for predicting transmembrane helices in protein sequences.Proc Int Conf Intell Syst Mol Biol 1998, 6:175-182. 57. Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.J Mol Biol 2001, 305:567-580. 58. Abascal F, Zardoya R, Posada D: ProtTest: selection of best-fit models of protein evolution.Bioinformatics 2005, 21:2104-2105. 59. Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.Syst Biol 2003, 52:696-704. 60. Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.Mol Biol Evol 2007, 24:1596-1599. 61. Primer 3 Software. Internet 2009 [http://primer3.sourceforge.net/]. 62. Danzmann RG, Cairney M, Davidson WS, Ferguson MM, Gharbi K, Guyomard R, et al: A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae).Genome 2005, 48:1037-1051. 63. Woram RA, Gharbi K, Sakamoto T, Hoyheim B, Holm LE, Naish K, et al: Comparative genome analysis of the primary sex-determining locus in salmonid fishes.Genome Res 2003, 13:272-280. 64. Danzmann RG: LINKMFEX: Linkage analysis package for outcrossed families with male of female exchange of the mapping parent, ver. 2.3. Internet 2006 [http://www.uoguelph.ca/~rdanzman/software/LINKMFEX/]. 65. National Animal Research Authority. Internet 2009 [http://www.fdu.no/]. 66. Schmittgen TD, Livak KJ: Analyzing real-time PCR data by the comparative C(T) method.Nat Protoc 2008, 3:1101-1108. doi:10.1186/1471-2164-11-154 Cite this article as: Lukacs et al.: Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon. BMC Genomics 2010 11:154. Page 17 of 17 Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color ﬁgure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit