Fig 1.
The part shown with a yellow background is the preprocessing stage of MIPE. The orange background details Stage I of the main program of MIPE, specifically sequence screening and taxonomy of a metagenome and a metatranscriptome, and the blue background describes steps used for metatranscriptomic sequence screening and taxonomy. The lake blue background details the steps associated with appending a reference sequence, locating and extracting primer binding sites, which form part of Stage I in the MIPE main program. The green background shows Stage II in the MIPE main program.
Fig 2.
(A) Match type file, “.Match_type”. The file contains each match type for the sequence, the sequence binding sites for the primers, the mismatch base numbers in total, the mismatch base numbers in last 4 bases, the matched degree, the completeness, the taxonomy information and the score. (B) Statistics file, “.Stat”. The file presents a summary of the primer evaluation, and all tables result from the analysis of the “Match_type” files. The file contains six tables: the match and mismatch sequence count, the distribution of completeness, the most frequent mismatch type, the most common match type, the count of each mismatch in every position, and the coverage over taxonomy levels. Rare biospheres can be found in “Table 6” of the statistics file and sequences whose completeness were less than one were not counted in this table. For more details, please see S3 Table.
Fig 3.
Linear correlation-based comparison of MG-RAST and MIPE.
Archaeal and bacterial read numbers used for linear correlation at the (A) phylum and (B) class levels. Taxa whose abundances are greater than 100 reads in either SILVA SSU (v119) or MG-RAST built-in SSU databases are listed separately, and the others are summed into one item.
Fig 4.
Coverage of the “SILVA test set” with the primers F515 (A) and R806 (B) obtained using MIPE and PrimerProspector. The SILVA test set sequences were derived from the SILVA SSU database (v104) and filtered at 97% sequence identity with Uclust. The y-axes represent the percent of coverage.