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Kristina Lang et al.
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CDD: NCBI's conserved domain database
Aron Marchler-Bauer et al.
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Abundant rifampin resistance genes and significant correlations of antibiotic resistance genes and plasmids in various environments revealed by metagenomic analysis
Liping Ma et al.
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Torsten Seemann
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Guillaume Borrel et al.
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Feng-Ping Wang et al.
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Jun Meng et al.
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Divya Prakash et al.
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Victor M. Markowitz et al.
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Emma J. Gagen et al.
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Karen G. Lloyd et al.
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Ting-Wen Cheng et al.
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The Sequence Read Archive
Rasko Leinonen et al.
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Erik Kristiansson et al.
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S. Kelly et al.
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Doug Hyatt et al.
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Ambrish Roy et al.
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Autotrophic carbon fixation in archaea
Ivan A. Berg et al.
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Infernal 1.0: inference of RNA alignments
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Morgan N. Price et al.
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Emily J. Beal et al.
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Robert K. Bradley et al.
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Ramy K. Aziz et al.
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Si Quang Le et al.
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DH Huson et al.
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KT Konstantinidis et al.
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RC Edgar
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W Ludwig et al.
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Anaerobic growth of Methanosarcina acetivorans C2A on carbon monoxide:: An unusual way of life for a methanogenic archaeon
M Rother et al.
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The TIGRFAMs database of protein families
DH Haft et al.
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The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill
PE Luton et al.
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A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
S Whelan et al.
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Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: Unusual amino acid modification, conservation and adaptation
WG Grabarse et al.
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K Rutherford et al.
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M Kanehisa et al.
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