9 Genomic Techniques and How to Apply Them to Marine Questions
373
Goesmann A, Linke B, Bartels D et al (2005) BRIGEP-the BRIDGE-based genome-transcriptomeproteome browser. Nucleic Acids Res 33:W710–W716
Goldberg SMD, Johnson J, Busam D et al (2006) A Sanger/pyrosequencing hybrid approach for
the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad
Sci U S A 103(30):11240–11245
Golub TR, Slonim DK, Tamayo P et al (1999) Molecular classification of cancer: class discovery
and class prediction by gene expression monitoring. Science 286(5439):531–537
Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome
Res 8(3):195–202
Gordon D, Desmarais C, Green P (2001) Automated finishing with autofinish. Genome Res
11(4):614–625
Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic
Acids Res 10(22):7055–7074
Green P (2002) Whole-genome disassembly. Proc Natl Acad Sci U S A 99(7):4143–4144
Gresham D, Ruderfer DM, Pratt SC et al (2006) Genome-wide detection of polymorphisms at
nucleotide resolution with a single DNA microarray. Science 311(5769):1932–1936
Gross SS, Brent MR (2006) Using multiple alignments to improve gene prediction. J Comput Biol
13(2):379–393
Guigo R, Reese MG (2005) EGASP: collaboration through competition to find human genes. Nat
Methods 2(8):575–577
Guigo R, Flicek P, Abril JF et al (2006) EGASP: the human ENCODE Genome Annotation
Assessment Project. Genome Biol 7(Suppl 1):S2–S31
Guo FB, Ou HY, Zhang CT (2003) ZCURVE: a new system for recognizing protein-coding genes
in bacterial and archaeal genomes. Nucleic Acids Res 31(6):1780–1789
Haas BJ, Salzberg SL, Zhu W et al (2008) Automated eukaryotic gene structure annotation
using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9(1):
R7
Henrick K, Feng Z, Bluhm WF et al (2008) Remediation of the protein data bank archive. Nucleic
Acids Res 36:D426–D433
Herring CD, Raghunathan A, Honisch C et al (2006) Comparative genome sequencing of
Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet
38(12):1406–1412
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9(9):868–877
Huang X, Adams MD, Zhou H et al (1997) A tool for analyzing and annotating genomic sequences.
Genomics 46(1):37–45
Iizuka M, Yamauchi M, Ando K et al (1994) Quantitative RT-PCR assay detecting the transcriptional induction of vascular endothelial growth factor under hypoxia. Biochem Biophys Res
Commun 205(2):1474–1480
Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol
7:138–148
Ju J, Kim DH, Bi L et al (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci U S A 103(52):
19635–19640
Kaiser O, Bartels D, Bekel T et al (2003) Whole genome shotgun sequencing guided by
bioinformatics pipelines-an optimized approach for an established technique. J Biotechnol
106(2–3):121–133
Kall L, Krogh A, Sonnhammer EL (2007) Advantages of combined transmembrane topology and
signal peptide prediction-the Phobius web server. Nucleic Acids Res 35:W429–W432
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res
28:27–30
Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12(4):656–664
Korf I (2004) Gene finding in novel genomes. BMC Bioinformatics 5:59
373
Goesmann A, Linke B, Bartels D et al (2005) BRIGEP-the BRIDGE-based genome-transcriptomeproteome browser. Nucleic Acids Res 33:W710–W716
Goldberg SMD, Johnson J, Busam D et al (2006) A Sanger/pyrosequencing hybrid approach for
the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad
Sci U S A 103(30):11240–11245
Golub TR, Slonim DK, Tamayo P et al (1999) Molecular classification of cancer: class discovery
and class prediction by gene expression monitoring. Science 286(5439):531–537
Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome
Res 8(3):195–202
Gordon D, Desmarais C, Green P (2001) Automated finishing with autofinish. Genome Res
11(4):614–625
Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic
Acids Res 10(22):7055–7074
Green P (2002) Whole-genome disassembly. Proc Natl Acad Sci U S A 99(7):4143–4144
Gresham D, Ruderfer DM, Pratt SC et al (2006) Genome-wide detection of polymorphisms at
nucleotide resolution with a single DNA microarray. Science 311(5769):1932–1936
Gross SS, Brent MR (2006) Using multiple alignments to improve gene prediction. J Comput Biol
13(2):379–393
Guigo R, Reese MG (2005) EGASP: collaboration through competition to find human genes. Nat
Methods 2(8):575–577
Guigo R, Flicek P, Abril JF et al (2006) EGASP: the human ENCODE Genome Annotation
Assessment Project. Genome Biol 7(Suppl 1):S2–S31
Guo FB, Ou HY, Zhang CT (2003) ZCURVE: a new system for recognizing protein-coding genes
in bacterial and archaeal genomes. Nucleic Acids Res 31(6):1780–1789
Haas BJ, Salzberg SL, Zhu W et al (2008) Automated eukaryotic gene structure annotation
using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9(1):
R7
Henrick K, Feng Z, Bluhm WF et al (2008) Remediation of the protein data bank archive. Nucleic
Acids Res 36:D426–D433
Herring CD, Raghunathan A, Honisch C et al (2006) Comparative genome sequencing of
Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet
38(12):1406–1412
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9(9):868–877
Huang X, Adams MD, Zhou H et al (1997) A tool for analyzing and annotating genomic sequences.
Genomics 46(1):37–45
Iizuka M, Yamauchi M, Ando K et al (1994) Quantitative RT-PCR assay detecting the transcriptional induction of vascular endothelial growth factor under hypoxia. Biochem Biophys Res
Commun 205(2):1474–1480
Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol
7:138–148
Ju J, Kim DH, Bi L et al (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci U S A 103(52):
19635–19640
Kaiser O, Bartels D, Bekel T et al (2003) Whole genome shotgun sequencing guided by
bioinformatics pipelines-an optimized approach for an established technique. J Biotechnol
106(2–3):121–133
Kall L, Krogh A, Sonnhammer EL (2007) Advantages of combined transmembrane topology and
signal peptide prediction-the Phobius web server. Nucleic Acids Res 35:W429–W432
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res
28:27–30
Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12(4):656–664
Korf I (2004) Gene finding in novel genomes. BMC Bioinformatics 5:59