68
A. Meyerdierks and F.O. Glöckner
Overbeek R, Larsen N, Pusch GD et al (2000) WIT: integrated system for high-throughput genome
sequence analysis and metabolic reconstruction. Nucleic Acids Res 28:123–125
Pace NR, Stahl DA, Olsen GJ et al (1985) Analyzing natural microbial populations by rRNA
sequences. ASM News 51:4–12
Park SJ, Kang CH, Chae JC et al (2008) Metagenome microarray for screening of fosmid clones
containing specific genes. FEMS Microbiol Lett 284:28–34
Pernthaler A, Dekas AE, Brown CT et al (2008) Diverse syntrophic partnerships from deep-sea
methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci U S A
105:7052–7057
Piel J (2002) A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial
symbiont of Paederus beetles. Proc Natl Acad Sci U S A 99:14002–14007
Pinard R, de Winter A, Sarkis GJ et al (2006) Assessment of whole genome amplification-induced
bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics
7:21
Podar M, Abulencia CB, Walcher M et al (2007) Targeted access to the genomes of low-abundance
organisms in complex microbial communities. Appl Environ Microbiol 73:3205–3214
Poretsky RS, Bano N, Buchan A et al (2005) Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol 71:4121–4126
Pride DT, Meinersmann RJ, Wassenaar TM et al (2003) Evolutionary implications of microbial
genome tetranucleotide frequency biases. Genome Res 13:145–158
Prober JM, Trainor GL, Dam RJ et al (1987) A system for rapid DNA sequencing with fluorescent
chain-terminating dideoxynucleotides. Science 238:336–341
Promega Corporation (2007) Technical Bulletin: Packagene
R
Lambda DNA Packaging System.
Pruesse E, Quast C, Knittel K et al (2007) SILVA: a comprehensive online resource for quality
checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res
35:7188–7196
Quaiser A, Ochsenreiter T, Klenk HP et al (2002) First insight into the genome of an uncultivated
crenarchaeote from soil. Environ Microbiol 4:603–611
Quaiser A, Ochsenreiter T, Lanz C et al (2003) Acidobacteria form a coherent but highly diverse
group within the bacterial domain: evidence from environmental genomics. Mol Microbiol
50:563–575
Quast C (2006) MicHanThi – design and implementation of a system for the prediction of gene
functions in genome annotation projects. Diploma thesis. Department of Computer Science
and Microbial Genomics Group. University Bremen and Max Planck Institute for Marine
Microbiology, Bremen
Raes J, Foerstner KU, Bork P (2007) Get the most out of your metagenome: computational analysis
of environmental sequence data. Curr Opin Microbiol 10:490–498
Raghunathan A, Ferguson HR, Bornarth CJ et al (2005) Genomic DNA amplification from a single
bacterium. Appl Environ Microbiol 71:3342–3347
Ram RJ, VerBerkmoes NC, Thelen MP et al (2005) Community proteomics of a natural microbial
biofilm. Science 308:1915–1920
Rappe MS, Connon SA, Vergin KL et al (2002) Cultivation of the ubiquitous SAR11 marine
bacterioplankton clade. Nature 418:630–633
Richter M, Lombardot T, Kostadinov I et al (2008) JCoast – A biologist-centric software tool for
data mining and comparison of prokaryotic (meta)genomes. BMC Bioinformatics 9:177
Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial
communities. Ann Rev Genet 38:525–552
Robidart JC, Bench SR, Feldman RA et al (2008) Metabolic versatility of the Riftia pachyptila
endosymbiont revealed through metagenomics. Environ Microbiol 10:727–737
Rogers YH, Venter JC (2005) Genomics – Massively parallel sequencing. Nature 437:326–327
Rondon MR, August PR, Bettermann AD et al (2000) Cloning the soil metagenome: a strategy
for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ
Microbiol 66:2541–2547
A. Meyerdierks and F.O. Glöckner
Overbeek R, Larsen N, Pusch GD et al (2000) WIT: integrated system for high-throughput genome
sequence analysis and metabolic reconstruction. Nucleic Acids Res 28:123–125
Pace NR, Stahl DA, Olsen GJ et al (1985) Analyzing natural microbial populations by rRNA
sequences. ASM News 51:4–12
Park SJ, Kang CH, Chae JC et al (2008) Metagenome microarray for screening of fosmid clones
containing specific genes. FEMS Microbiol Lett 284:28–34
Pernthaler A, Dekas AE, Brown CT et al (2008) Diverse syntrophic partnerships from deep-sea
methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci U S A
105:7052–7057
Piel J (2002) A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial
symbiont of Paederus beetles. Proc Natl Acad Sci U S A 99:14002–14007
Pinard R, de Winter A, Sarkis GJ et al (2006) Assessment of whole genome amplification-induced
bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics
7:21
Podar M, Abulencia CB, Walcher M et al (2007) Targeted access to the genomes of low-abundance
organisms in complex microbial communities. Appl Environ Microbiol 73:3205–3214
Poretsky RS, Bano N, Buchan A et al (2005) Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol 71:4121–4126
Pride DT, Meinersmann RJ, Wassenaar TM et al (2003) Evolutionary implications of microbial
genome tetranucleotide frequency biases. Genome Res 13:145–158
Prober JM, Trainor GL, Dam RJ et al (1987) A system for rapid DNA sequencing with fluorescent
chain-terminating dideoxynucleotides. Science 238:336–341
Promega Corporation (2007) Technical Bulletin: Packagene
R
Lambda DNA Packaging System.
Pruesse E, Quast C, Knittel K et al (2007) SILVA: a comprehensive online resource for quality
checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res
35:7188–7196
Quaiser A, Ochsenreiter T, Klenk HP et al (2002) First insight into the genome of an uncultivated
crenarchaeote from soil. Environ Microbiol 4:603–611
Quaiser A, Ochsenreiter T, Lanz C et al (2003) Acidobacteria form a coherent but highly diverse
group within the bacterial domain: evidence from environmental genomics. Mol Microbiol
50:563–575
Quast C (2006) MicHanThi – design and implementation of a system for the prediction of gene
functions in genome annotation projects. Diploma thesis. Department of Computer Science
and Microbial Genomics Group. University Bremen and Max Planck Institute for Marine
Microbiology, Bremen
Raes J, Foerstner KU, Bork P (2007) Get the most out of your metagenome: computational analysis
of environmental sequence data. Curr Opin Microbiol 10:490–498
Raghunathan A, Ferguson HR, Bornarth CJ et al (2005) Genomic DNA amplification from a single
bacterium. Appl Environ Microbiol 71:3342–3347
Ram RJ, VerBerkmoes NC, Thelen MP et al (2005) Community proteomics of a natural microbial
biofilm. Science 308:1915–1920
Rappe MS, Connon SA, Vergin KL et al (2002) Cultivation of the ubiquitous SAR11 marine
bacterioplankton clade. Nature 418:630–633
Richter M, Lombardot T, Kostadinov I et al (2008) JCoast – A biologist-centric software tool for
data mining and comparison of prokaryotic (meta)genomes. BMC Bioinformatics 9:177
Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial
communities. Ann Rev Genet 38:525–552
Robidart JC, Bench SR, Feldman RA et al (2008) Metabolic versatility of the Riftia pachyptila
endosymbiont revealed through metagenomics. Environ Microbiol 10:727–737
Rogers YH, Venter JC (2005) Genomics – Massively parallel sequencing. Nature 437:326–327
Rondon MR, August PR, Bettermann AD et al (2000) Cloning the soil metagenome: a strategy
for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ
Microbiol 66:2541–2547