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the authors should add citations for the following references to access the complete reference list report - to access the complete reference list please go to the link above genome sequences of the nine myxobacteria species comparative genomic sequence of strain myxococcus xanthus dk1622 kyoto encyclopedia of genes and genomes pathways
table 2: it is stated that the accessory genes were identified by using blast. this is not an optimal method to identify accessory genes. it is important to use specialized software, like prokka , because blast returns false positive when the distance between two query sequences are less than 50bp. this is crucial given that a typical accessory gene has less than 50bp.
ankarsidya et al. propose a new method to determine the core and accessory gene content of genomes. this is superior to blast because it can identify core genes with low precision but high recall, like the 16s rrna, 23s rrna and trna genes. a third advantage is that it can identify genes closer than 50bp apart. while this method is more advanced than blast, it still has two issues. the software is expensive and not optimized for prokaryotic genomes. while this is not a problem for the quality of this work, in larger scale applications this becomes a significant limiting factor.
an ad hoc method to determine the core gene content is listed under methods. the authors state that they performed blast searches against 1435 non-redundant pdb files to identify homologs of the core gene clusters. the authors should cite the number of homologs, and perform a statistical analysis to determine the true proportion of non-core genes to determine that the number is within the 95% confidence interval. 3d9ccd7d82