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      CH4 production and oxidation processes in a boreal fen ecosystem after long-term water table drawdown : CH4 PRODUCTION AND OXIDATION PROCESSES

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          Most cited references 37

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          ProtTest: selection of best-fit models of protein evolution.

          Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. ProtTest is available under the GNU license from http://darwin.uvigo.es
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            Gapped BLAST and PSI BLAST—a new generation of protein data base search programs

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              The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill.

              Inferred amino acid sequences of the methyl coenzyme-M reductase (mcrA) gene from five different methanogen species were aligned and two regions with a high degree of homology flanking a more variable region were identified. Analysis of the DNA sequences from the conserved regions yielded two degenerate sequences from which a forward primer, a 32-mer, and a reverse primer, a 23-mer, could be derived for use in the specific PCR-based detection of methanogens. The primers were successfully evaluated against 23 species of methanogen representing all five recognized orders of this group of Archaea, generating a PCR product between 464 and 491 bp. Comparisons between the mcrA and 16S small subunit rRNA gene sequences using PHYLIP demonstrated that the tree topologies were strikingly similar. Methods were developed to enable the analysis of methanogen populations in landfill using the mcrA gene as the target. Two landfill sites were examined and 63 clones from a site in Mucking, Essex, and 102 from a site in Odcombe, Somerset, were analysed. Analysis revealed a far greater diversity in the methanogen population within landfill material than has been seen previously.
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                Author and article information

                Journal
                Global Change Biology
                Wiley-Blackwell
                13541013
                March 2011
                March 2011
                : 17
                : 3
                : 1311-1320
                Article
                10.1111/j.1365-2486.2010.02290.x
                © 2011

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