9 Genomic Techniques and How to Apply Them to Marine Questions
377
Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain-terminating inhibitors. Proc
Natl Acad Sci USA 74:5463–5467
Schena M, Shalon D, Davis RW et al (1995) Quantitative monitoring of gene expression patterns
with a complementary DNA microarray. Science 270(5235):467–470
Schiex T, Moisan A, Rouzé P (2001) Eugène: an eukaryotic gene finder that combines several
sources of evidence. In: Computational Biology, selected papers from JOBIM 2000 number
2066 in LNCS, Springer Verlag, New York, pp. 111–125.
Schneiker S, Martins dos Santos VA, Bartels D et al (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol
24(8):997–1004
Schneiker S, Perlova O, Kaiser O et al (2007) Complete genome sequence of the myxobacterium
Sorangium cellulosum. Nat Biotechnol 25(11):1281–1289
Shendure J, Mitra RD, Varma C et al (2004) Advanced sequencing technologies: methods and
goals. Nat Rev Genet 5(5):335–344
Shendure J, Porreca GJ, Reppas NB et al (2005) Accurate multiplex polony sequencing of an
evolved bacterial genome. Science 309(5741):1728–1732
Shendure JA, Porreca GJ, Church GM (2008) Overview of DNA sequencing strategies. Curr Protoc
Mol Biol Chapter 7: Unit 7:1
Skovgaard M, Jensen LJ, Brunak S et al (2001) On the total number of genes and their length
distribution in complete microbial genomes. Trends Genet 17(8):425–428
Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31
Smith MW, Feng DF, Doolittle RF (1992) Evolution by acquisition: the case for horizontal gene
transfers. Trends Biochem Sci 17(12):489–493
Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol
147(1):195–197
Sonnhammer EL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6:
175–182
Spellman PT, Miller M, Stewart J et al (2002) Design and implementation of microarray gene
expression markup language (MAGE-ML). Genome Biol 3(9): RESEARCH0046.
Stanke M, Waack S (2003) Gene prediction with a hidden Markov model and a new intron
submodel. Bioinformatics 19(Suppl 2):ii215–ii225
Stanke M, Tzvetkova A, Morgenstern B (2006) AUGUSTUS at EGASP: using EST, protein and
genomic alignments for improved gene prediction in the human genome. Genome Biol 7(Suppl
1):S11–S18
Sturn A, Quackenbush J, Trajanoski Z (2002) Genesis: cluster analysis of microarray data.
Bioinformatics 18(1):207–208
Sugawara H, Ogasawara O, Okubo K et al (2008) DDBJ with new system and face. Nucleic Acids
Res 36:D22–D24
Suzek BE, Ermolaeva MD, Schreiber M et al (2001) A probabilistic method for identifying start
codons in bacterial genomes. Bioinformatics 17(12):1123–1130
Tamames J, Casari G, Ouzounis C et al (1997) Conserved clusters of functionally related genes in
two bacterial genomes. Mol Evol 44:66–73
Tatsuov RL, Mushegian AR, Bork P et al (1996) Metabolism and evolution of Haemophilus
influenza deduced from a whole-genome comparison with Escherichia coli. Curr Biol
6(3):279–291
Tatusov RL, Fedorova ND, Jackson JD et al (2003) The COG database: an updated version includes
eukaryotes. BMC Bioinformatics 4:41
Team RDC (2008) R: a language and environment for statistical computing. R Foundation for
Statistical Computing, Vienna, Austria.
Tech M, Meinicke P (2006) An unsupervised classification scheme for improving predictions of
prokaryotic TIS. BMC Bioinformatics 7:121
377
Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain-terminating inhibitors. Proc
Natl Acad Sci USA 74:5463–5467
Schena M, Shalon D, Davis RW et al (1995) Quantitative monitoring of gene expression patterns
with a complementary DNA microarray. Science 270(5235):467–470
Schiex T, Moisan A, Rouzé P (2001) Eugène: an eukaryotic gene finder that combines several
sources of evidence. In: Computational Biology, selected papers from JOBIM 2000 number
2066 in LNCS, Springer Verlag, New York, pp. 111–125.
Schneiker S, Martins dos Santos VA, Bartels D et al (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol
24(8):997–1004
Schneiker S, Perlova O, Kaiser O et al (2007) Complete genome sequence of the myxobacterium
Sorangium cellulosum. Nat Biotechnol 25(11):1281–1289
Shendure J, Mitra RD, Varma C et al (2004) Advanced sequencing technologies: methods and
goals. Nat Rev Genet 5(5):335–344
Shendure J, Porreca GJ, Reppas NB et al (2005) Accurate multiplex polony sequencing of an
evolved bacterial genome. Science 309(5741):1728–1732
Shendure JA, Porreca GJ, Church GM (2008) Overview of DNA sequencing strategies. Curr Protoc
Mol Biol Chapter 7: Unit 7:1
Skovgaard M, Jensen LJ, Brunak S et al (2001) On the total number of genes and their length
distribution in complete microbial genomes. Trends Genet 17(8):425–428
Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31
Smith MW, Feng DF, Doolittle RF (1992) Evolution by acquisition: the case for horizontal gene
transfers. Trends Biochem Sci 17(12):489–493
Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol
147(1):195–197
Sonnhammer EL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6:
175–182
Spellman PT, Miller M, Stewart J et al (2002) Design and implementation of microarray gene
expression markup language (MAGE-ML). Genome Biol 3(9): RESEARCH0046.
Stanke M, Waack S (2003) Gene prediction with a hidden Markov model and a new intron
submodel. Bioinformatics 19(Suppl 2):ii215–ii225
Stanke M, Tzvetkova A, Morgenstern B (2006) AUGUSTUS at EGASP: using EST, protein and
genomic alignments for improved gene prediction in the human genome. Genome Biol 7(Suppl
1):S11–S18
Sturn A, Quackenbush J, Trajanoski Z (2002) Genesis: cluster analysis of microarray data.
Bioinformatics 18(1):207–208
Sugawara H, Ogasawara O, Okubo K et al (2008) DDBJ with new system and face. Nucleic Acids
Res 36:D22–D24
Suzek BE, Ermolaeva MD, Schreiber M et al (2001) A probabilistic method for identifying start
codons in bacterial genomes. Bioinformatics 17(12):1123–1130
Tamames J, Casari G, Ouzounis C et al (1997) Conserved clusters of functionally related genes in
two bacterial genomes. Mol Evol 44:66–73
Tatsuov RL, Mushegian AR, Bork P et al (1996) Metabolism and evolution of Haemophilus
influenza deduced from a whole-genome comparison with Escherichia coli. Curr Biol
6(3):279–291
Tatusov RL, Fedorova ND, Jackson JD et al (2003) The COG database: an updated version includes
eukaryotes. BMC Bioinformatics 4:41
Team RDC (2008) R: a language and environment for statistical computing. R Foundation for
Statistical Computing, Vienna, Austria.
Tech M, Meinicke P (2006) An unsupervised classification scheme for improving predictions of
prokaryotic TIS. BMC Bioinformatics 7:121