Cbcb:Pop-Lab:Papers: Difference between revisions
Jump to navigation
Jump to search
mNo edit summary |
|||
| Line 10: | Line 10: | ||
# 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** OTU picker (unpublished) | |||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 | |||
Revision as of 16:29, 19 February 2009
Metagenomics Reviews
- V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. A Bioinformatician's guide to Metagenomics.
- Clarridge J.E. 16S sequencing and clinical microbiology review
- C. Riesenfield, P. Schloss, and J. Handelsman. 2004 Metagenomics review.
- J. Eisen. Light metagenomics review for GOS expedition.
Pioneering papers
- G Muyzer, E C de Waal and A G Uitterlinden 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 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