Taxonomic classification of genes was performed based on the National Center for Biotechnology Information non-redundant nucleotide (NCBI-NT, downloaded at Aug. 2018) database. We aligned about 11 million genes of iHSMGC onto the NCBI-NT using BLASTN (v2.7.1, default parameters except that -evalue 1e-10 outfmt 6 -word_size 16). At least 70% alignment coverage of each gene was required. For multiple best-hits (from NCBI-NT database) mapping for the same gene with the same %identity, e value and bit score, we have used the following strategy:

We performed statistics on multiple best-hits (from NCBI-NT database) mapping for the same gene, including the number of annotated species present, the number of occurrences of each annotated species, and the average similarity of the same species. After completion of the statistics, the species annotation with the highest frequency and the highest average similarity was defined as the annotation of the gene. In case that different species for a single gene ranked the same in the statistics, we have chosen the species annotation that ordered first (i.e., the order of blast hits and e value). Accordingly, 95% identity was used as the critical value for species assignment, 85% identity was used as the critical value for genus assignment, and 65% for phylum assignment [6]. The 3.97 million genes of the gene catalog were annotated taxonomically.

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