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== Metagenomics Reviews ==
== Metagenomics Reviews ==


# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557| A Bioinformatician's guide to Metagenomics].
# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62| 16S sequencing and clinical microbiology review]
# Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]
# C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216  2004 Metagenomics review].
# J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082  Light metagenomics review for GOS expedition].
# Tringe SG, Hugenholtz P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4TMMGNR-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=bf695cb5d00fc3cd86640b8fc00c66b2 A renaissance for the pioneering 16S rRNA gene]
# Warnecke F, Hugenholtz P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18177506 Building on basic metagenomics with complementary technologies]
# Raes J, Foerstner KU, Bork P. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYRKN8-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=2f1854ad7b9c657576e4f6805031e602 Get the most out of your metagenome: computational analysis of environmental sequence data.]
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities]
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges]
# Ward N. [http://www3.interscience.wiley.com/cgi-bin/fulltext/118595942/HTMLSTART New directions and interactions in metagenomics research]
#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples]
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms]
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.]


== Pioneering papers ==
== Pioneering papers ==


# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695| PCR amplifying 16S rRNA genes and DGGE]
# G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract| Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]
# D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]
 
== 16S sequence analysis ==
* ''Classification.''
** RDP classifier
** BLAST searches
** Multilocus classification
** Sogin-like database search methods
** Sanger ''vs.'' 454
* ''Alignment.''
** ClustalW
** NAST
** MUSCLE
** Pairwise
** Masking approaches (LaneMask)
* ''Distance corrections.''
** Jukes-Cantor
** Kimura-2
** Felsenstein84
** Olsen
* ''Clustering.''
** DOTUR
** VI-cut
** OTU picker (unpublished)
** Database versions (Sogin papers)
* ''Community comparison.''
** Diversity estimators
** Rarefaction curves
** DOTUR
** EstimateS
** SONs
** TreeClimber
** S-libshuff
** UniFrac
** MEGAN
** Xipe - single sample comparisons
** Metastats
 
== DNA sequence binning ==
# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)
# [http://arxiv.org/abs/0708.3098 CompostBin] Principle Component Analysis (PCA)
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18218139 AMI] Mutual Information
# [http://www.ncbi.nlm.nih.gov/pubmed/18535082?dopt=Citation HSOM] Hierarchical Sef-Organizing Map
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18442374 GSOM] Growing SOM
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18285365 CARMA] Pfam and Phylogeny
# [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples] REVIEW

Latest revision as of 18:23, 19 February 2009

Metagenomics Reviews

  1. V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. A Bioinformatician's guide to Metagenomics.
  2. Clarridge J.E. 16S sequencing and clinical microbiology review
  3. C. Riesenfield, P. Schloss, and J. Handelsman. 2004 Metagenomics review.
  4. J. Eisen. Light metagenomics review for GOS expedition.
  5. Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene
  6. Warnecke F, Hugenholtz P. Building on basic metagenomics with complementary technologies
  7. Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental sequence data.
  8. Kevin Chen, Lior Pachter Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
  9. Foerstner KU, von Mering C, Bork P. Comparative analysis of environmental sequences: potential and challenges
  10. Ward N. New directions and interactions in metagenomics research
  11. Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples
  12. Handelsman J. Metagenomics: Application of Genomics to Uncultured Microorganisms
  13. Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities.

Pioneering papers

  1. G Muyzer, E C de Waal and A G Uitterlinden PCR amplifying 16S rRNA genes and DGGE
  2. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

16S sequence analysis

  • Classification.
    • RDP classifier
    • BLAST searches
    • Multilocus classification
    • Sogin-like database search methods
    • Sanger vs. 454
  • Alignment.
    • ClustalW
    • NAST
    • MUSCLE
    • Pairwise
    • Masking approaches (LaneMask)
  • Distance corrections.
    • Jukes-Cantor
    • Kimura-2
    • Felsenstein84
    • Olsen
  • Clustering.
    • DOTUR
    • VI-cut
    • OTU picker (unpublished)
    • Database versions (Sogin papers)
  • Community comparison.
    • Diversity estimators
    • Rarefaction curves
    • DOTUR
    • EstimateS
    • SONs
    • TreeClimber
    • S-libshuff
    • UniFrac
    • MEGAN
    • Xipe - single sample comparisons
    • Metastats

DNA sequence binning

  1. Phylopythia Support Vector Machine (SVM)
  2. CompostBin Principle Component Analysis (PCA)
  3. AMI Mutual Information
  4. HSOM Hierarchical Sef-Organizing Map
  5. GSOM Growing SOM
  6. CARMA Pfam and Phylogeny
  7. What's in the mix: phylogenetic classification of metagenome sequence samples REVIEW
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