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. 2011 Dec 12;6(12):e28388. doi: 10.1371/journal.pone.0028388

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Halachev et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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xBASE-Orth has a significant speed advantage over direct application of OrthoMCL which comes at the possible cost of decreased accuracy. We compared the performance of the two approaches over three distinct phyla – Bacteroidetes (40 complete genomes), Cyanobacteria (41 genomes) and Euryarchaeota (62 genomes), computing orthologs at genus, family, order and phylum level. At higher taxonomic levels the pan-genome sizes are significantly smaller compared to the full CDS collections - about half at order level and only about one third at phylum level for the datasets analyzed here (CR stands for Compression Ratio = [Number of CDSs in pan-genomes used by xBASE-Orth/Number of CDSs used by OrthoMCL] * 100%). Hence, at higher levels each CDS in a pan-genome is a representative of a larger set of orthologous/paralogous CDSs, plausibly becoming less sensitive and specific. Compared to the OrthoMCL results, it appears that on average the xBASE-Orth results contain from 1% (at genus level) to 9.7% (phylum) additional ortholog pairs, while failing to detect from 0.5% (genus) to 14% (phylum) OrthoMCL pairs.