Computational protocol: Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli

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Protocol publication

[…] Complete genomic sequences and initial annotations were obtained from NCBI ([]; June 2011). Multiple sequence alignments were made with ClustalX [], and BioEdit [] was used to analyze sequences and alignments. Specific bootstrapped neighbor-joining trees, with ‘correction for multiple substitutions’, were created using ClustalX and the trees were analyzed using LOFT [] and Dendroscope []. The Microbial Genome Viewer 2.0 (http://mgv2.cmbi.ru.nl) was used to examine the function information within the genomic context. Frequency representations of aligned sequences were created with Weblogo []. Microarray data from glnR gene knockouts in Streptococcus pneumoniae and Streptococcus mutans used in this research were extracted from the Gene Expression Omnibus from NCBI [].The raw data resulting from the various analyses can be found at http://www.cmbi.ru.nl/bamics/supplementary/GrootKormelinketal_2012_GlnRregulon/. Data file 1: GlnR and TnrA motifs used for SMS; data file 2: GlnR motif search in Bacilli (w/o Streptococci); data file 3: GlnR motif search in Streptococci; data file 4: GlnR and TnrA motif search in Bacillus subtilis. […]

Pipeline specifications

Software tools Clustal W, BioEdit, LOFT, Dendroscope, WebLogo
Databases GEO
Applications Genome annotation, Phylogenetics, Genome data visualization
Chemicals Ammonia, Nitrogen