9 Genomic Techniques and How to Apply Them to Marine Questions
375
Mangalam H (2002) The Bio∗ toolkits-a brief overview. Brief Bioinform 3(3):296–302
Mao X, Cai T, Olyarchuk JG et al (2005) Automated genome annotation and pathway identification
using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19):3787–3793
Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet
9:387–402
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437(7057):376–380
Mathe C, Sagot MF, Schiex T et al (2002) Current methods of gene prediction, their strengths and
weaknesses. Nucleic Acids Res 30(19):4103–4117
Matsumura H, Reich S, Ito A et al (2003) Gene expression analysis of plant host-pathogen
interactions by SuperSAGE. Proc Natl Acad Sci U S A 100(26):15718–15723
Maurer M, Molidor R, Sturn A et al (2005) MARS: microarray analysis, retrieval, and storage
system. BMC Bioinformatics 6:101
McHardy AC, Pühler A, Kalinowski J et al (2004a) Comparing expression level-dependent features in codon usage with protein abundance: an analysis of predictive proteomics . Proteomics
4(1):46–58
McHardy AC, Goesmann A, Pühler A et al (2004b) Development of joint application strategies for
two microbial gene finders. Bioinformatics 20(10):1622–1631
Meyer F, Goesmann A, McHardy AC et al (2003) GenDB-an open source genome annotation
system for prokaryote genomes. Nucleic Acids Res 31(8):2187–2195
Millar CD, Huynen L, Subramanian S et al (2008) New developments in ancient genomics. Trends
Ecol Evol 23(7):386–393
Miron M, Nadon R (2006) Inferential literacy for experimental high-throughput biology. Trends
Genet 22(2):84–89
Moore JE, Lake JA (2003) Gene structure prediction in syntenic DNA segments. Nucleic Acids
Res 31(24):7271–7279
Mott R (1997) EST_GENOME: a program to align spliced DNA sequences to unspliced genomic
DNA. Comput Appl Biosci 13(4):477–478
Mulder NJ, Apweiler R, Attwood TK et al (2007) New developments in the InterPro database.
Nucleic Acids Res 35:D224–D228
Nagaraj SH, Deshpande N, Gasser RB et al (2007) ESTExplorer: an expressed sequence tag (EST)
assembly and annotation platform. Nucleic Acids Res 35:W143–W147
Nakano M, Komatsu J, Matsuura S-i et al (2003) Single-molecule PCR using water-in-oil
emulsion. J Biotechnol 102(2): 117–124
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in
the amino acid sequence of two proteins. J Mol Biol 48(3):443–453
Nekrutenko A, Chung WY, Li WH (2003) ETOPE: evolutionary test of predicted exons. Nucleic
Acids Res 31(13):3564–3567
Ng P, Wei C-L, Sung W-K et al (2005) Gene identification signature (GIS) analysis for
transcriptome characterization and genome annotation. Nat Methods 2(2):105–111
Ng P, Tan JJS, Ooi HS et al (2006) Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res
34(12):e84
Noguchi H, Park J, Takagi T (2006) MetaGene: prokaryotic gene finding from environmental
genome shotgun sequences. Nucleic Acids Res 34(19):5623–5630
Ou HY, Guo FB, Zhang CT (2004) GS-Finder: a program to find bacterial gene start sites with a
self-training method. Int J Biochem Cell Biol 36(3):535–544
Overbeek R, Disz T, Stevens R (2004) The SEED: a peer-to-peer environment for genome
annotation. Commun ACM 47(11):47–51
Overbeek R, Fonstein M, D‘Souza M et al (1999) The use of gene clusters to infer functional
coupling. Proc Natl Acad Sci U S A 96:2896–2901
Overbeek R, Larsen N, Pusch GD et al (2000) WIT: integrated system for high-throughput genome
sequence analysis and metabolic reconstruction. Nucleic Acids Res 28(1):123–125
375
Mangalam H (2002) The Bio∗ toolkits-a brief overview. Brief Bioinform 3(3):296–302
Mao X, Cai T, Olyarchuk JG et al (2005) Automated genome annotation and pathway identification
using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19):3787–3793
Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet
9:387–402
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437(7057):376–380
Mathe C, Sagot MF, Schiex T et al (2002) Current methods of gene prediction, their strengths and
weaknesses. Nucleic Acids Res 30(19):4103–4117
Matsumura H, Reich S, Ito A et al (2003) Gene expression analysis of plant host-pathogen
interactions by SuperSAGE. Proc Natl Acad Sci U S A 100(26):15718–15723
Maurer M, Molidor R, Sturn A et al (2005) MARS: microarray analysis, retrieval, and storage
system. BMC Bioinformatics 6:101
McHardy AC, Pühler A, Kalinowski J et al (2004a) Comparing expression level-dependent features in codon usage with protein abundance: an analysis of predictive proteomics . Proteomics
4(1):46–58
McHardy AC, Goesmann A, Pühler A et al (2004b) Development of joint application strategies for
two microbial gene finders. Bioinformatics 20(10):1622–1631
Meyer F, Goesmann A, McHardy AC et al (2003) GenDB-an open source genome annotation
system for prokaryote genomes. Nucleic Acids Res 31(8):2187–2195
Millar CD, Huynen L, Subramanian S et al (2008) New developments in ancient genomics. Trends
Ecol Evol 23(7):386–393
Miron M, Nadon R (2006) Inferential literacy for experimental high-throughput biology. Trends
Genet 22(2):84–89
Moore JE, Lake JA (2003) Gene structure prediction in syntenic DNA segments. Nucleic Acids
Res 31(24):7271–7279
Mott R (1997) EST_GENOME: a program to align spliced DNA sequences to unspliced genomic
DNA. Comput Appl Biosci 13(4):477–478
Mulder NJ, Apweiler R, Attwood TK et al (2007) New developments in the InterPro database.
Nucleic Acids Res 35:D224–D228
Nagaraj SH, Deshpande N, Gasser RB et al (2007) ESTExplorer: an expressed sequence tag (EST)
assembly and annotation platform. Nucleic Acids Res 35:W143–W147
Nakano M, Komatsu J, Matsuura S-i et al (2003) Single-molecule PCR using water-in-oil
emulsion. J Biotechnol 102(2): 117–124
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in
the amino acid sequence of two proteins. J Mol Biol 48(3):443–453
Nekrutenko A, Chung WY, Li WH (2003) ETOPE: evolutionary test of predicted exons. Nucleic
Acids Res 31(13):3564–3567
Ng P, Wei C-L, Sung W-K et al (2005) Gene identification signature (GIS) analysis for
transcriptome characterization and genome annotation. Nat Methods 2(2):105–111
Ng P, Tan JJS, Ooi HS et al (2006) Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res
34(12):e84
Noguchi H, Park J, Takagi T (2006) MetaGene: prokaryotic gene finding from environmental
genome shotgun sequences. Nucleic Acids Res 34(19):5623–5630
Ou HY, Guo FB, Zhang CT (2004) GS-Finder: a program to find bacterial gene start sites with a
self-training method. Int J Biochem Cell Biol 36(3):535–544
Overbeek R, Disz T, Stevens R (2004) The SEED: a peer-to-peer environment for genome
annotation. Commun ACM 47(11):47–51
Overbeek R, Fonstein M, D‘Souza M et al (1999) The use of gene clusters to infer functional
coupling. Proc Natl Acad Sci U S A 96:2896–2901
Overbeek R, Larsen N, Pusch GD et al (2000) WIT: integrated system for high-throughput genome
sequence analysis and metabolic reconstruction. Nucleic Acids Res 28(1):123–125