Bioinformatics 2007, 23:673–679.PubMedCrossRef 126. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. selleck Nucleic Acids Res 1997, 25:3389–3402.PubMedCrossRef 127. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955–964.PubMedCrossRef 128. Katoh K, Asimenos G, Toh H: Multiple JAK inhibitor alignment of DNA sequences with MAFFT. Methods Mol Biol 2009, 537:39–64.PubMedCrossRef 129. Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic

analysis. Mol Biol Evol 2000, 17:540–552.PubMed 130. Bryant D, Moulton V: Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 2004, 21:255–265.PubMedCrossRef 131. Huson DH, Bryant D: Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006, 23:254–267.PubMedCrossRef 132. Marchler-Bauer A, Panchenko

AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH: CDD: a database of conserved domain alignments with links SN-38 to domain three-dimensional structure. Nucleic Acids Res 2002, 30:281–283.PubMedCrossRef 133. Cvetkovic A, Menon AL, Thorgersen MP, Scott JW, Poole FL, Jenney FE Jr, Lancaster WA, Praissman JL, Shanmukh S, Vaccaro BJ, Trauger SA, Kalisiak E, Apon JV, Siuzdak G, Yannone SM, Tainer JA, Adams MW: Microbial metalloproteomes are largely uncharacterized. Nature 2010, 466:779–782.PubMedCrossRef 134.

Vernikos GS, Parkhill J: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 2006, 22:2196–2203.PubMedCrossRef 135. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673–4680.PubMedCrossRef 136. Loytynoja A, Goldman N: An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci USA 2005, 102:10557–10562.PubMedCrossRef 137. R Development Core Team: R: A language and environment for statistical computing. [http://​www.​R-project.​org/​] Nutlin-3 mouse R Foundation for Statistical Computing, Vienna, Austria 2010. 138. Ren S, Higashi H, Lu H, Azuma T, Hatakeyama M: Structural basis and functional consequence of Helicobacter pylori CagA multimerization in cells. J Biol Chem 2006, 281:32344–32352.PubMedCrossRef 139. Devi SH, Taylor TD, Avasthi TS, Kondo S, Suzuki Y, Megraud F, Ahmed N: Genome of Helicobacter pylori strain 908. J Bacteriol 2010, 192:6488–6489.PubMedCrossRef 140. Xia Y, Yamaoka Y, Zhu Q, Matha I, Gao X: A comprehensive sequence and disease correlation analyses for the C-terminal region of CagA protein of Helicobacter pylori . PLoS One 2009, 4:e7736.PubMedCrossRef 141.