PMC:3395577 / 27080-28296 JSONTXT

{"project":"MicrobeTaxon","denotations":[{"id":"T54","span":{"begin":59,"end":66},"obj":"562"}],"namespaces":[{"prefix":"_base","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Phylogenies analysis of BGL\nThe condon usage preference of E. coli in translation initiation region of pET-20-BGL was analyzed by using codon usage tool (http://gcua.schoedl.de/). The potential ORF of bgl was searched using the ORF search tool provided by the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov). Database searching was performed with Blast at NCBI and against CAZy (http://www.cazy.org). The active site of the enzyme was analyzed with the prosite tool (http://prosite.expasy.org/scanprosite). The multiple sequence alignment tool Clustal X2.0 was used for multiple protein sequence alignment [27]. Sequences were further edited and aligned manually, when necessary, using the Mega 5 for editing. For phylogenetic analyses of conserved domains, sequences were trimmed so that only the relevant protein domains remained in the alignment [28]. Phylogenetic relationships were inferred using the Neighbor-Joining (NJ) and Maximum-Parsimony (MP) method as implemented in Paup 4.0 for the NJ and MP trees, the results were evaluated with 1000 bootstrap replicates [29]. The generated trees were displayed using TREEVIEW 1.6.6 (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html)."}

{"project":"2_test","denotations":[{"id":"22571470-17846036-7770712","span":{"begin":635,"end":637},"obj":"17846036"},{"id":"22571470-21546353-7770713","span":{"begin":878,"end":880},"obj":"21546353"}],"text":"Phylogenies analysis of BGL\nThe condon usage preference of E. coli in translation initiation region of pET-20-BGL was analyzed by using codon usage tool (http://gcua.schoedl.de/). The potential ORF of bgl was searched using the ORF search tool provided by the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov). Database searching was performed with Blast at NCBI and against CAZy (http://www.cazy.org). The active site of the enzyme was analyzed with the prosite tool (http://prosite.expasy.org/scanprosite). The multiple sequence alignment tool Clustal X2.0 was used for multiple protein sequence alignment [27]. Sequences were further edited and aligned manually, when necessary, using the Mega 5 for editing. For phylogenetic analyses of conserved domains, sequences were trimmed so that only the relevant protein domains remained in the alignment [28]. Phylogenetic relationships were inferred using the Neighbor-Joining (NJ) and Maximum-Parsimony (MP) method as implemented in Paup 4.0 for the NJ and MP trees, the results were evaluated with 1000 bootstrap replicates [29]. The generated trees were displayed using TREEVIEW 1.6.6 (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html)."}