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Example sentences for: msu
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The following sequences were used for the 16S rRNA phylogeny (the sequences are available under these names from the Ribosomal Database Project II http://rdp.cme.msu.edu/: Sul.solfa4, Sul.acalda, Ap.pernixl, Mc.thlitho, Mc.janrrnA, Mb.tautot2, Pc.furios2, Pc.abyssi, AP000001, AB016298, Tpl.acidop, Arg.fulgid p, Hf.volcani, Hb.spCh2_2, Hb.salina2, Msr.mazei5, Msr.barke2, Dco.mobili.
RNA secondary structure of the ThiF domain coding regions of the sequences in the high homology group was predicted using the GeneBee web server http://www.genebee.msu.su/using both individual sequences as well as alignments [ 45 ] .
The aligned small subunit ribosomal RNA sequences were retrieved from the Ribosomal Database Project II http://rdp.cme.msu.edu [ 44 ] . Francine Perler (New England Biolabs) the curator of the intein database http://www.neb.com/inteins/int_reg.htmlkindly provided the sequences of all known inteins.
An alignment output from this source was used to create a dendrogram using TreeTop [ 45 ] with PHYLIP output (default parameters) at a node of the European Molecular Biology Network http://www.genebee.msu.su [ 47 ] . Potential phosphorylation sites were identified using NetPhos 2.0 http://www.cbs.dtu.dk/services/NetPhos [ 48 ] . After alignment with CLUSTAL W, identical and similar amino acids in Figure 3were identified using MacBoxshade 2.15 http://www.isrec.isb-sib.ch/ftp-server/boxshade/MacBoxshade.
A third way that large libraries are often dereplicated requires submitting the sequences as batch files to a database (either local or remote), then searching the same sequences against the updated database using BLAST or Sequence Similarity http://www.cme.msu.edu/RDP/docs/sim_matrix_issues.html.
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