MIPE: Metagenome based community structure explorer and primer evaluation tool
MIPE (MIcrobiota Prior knowledge Explorer) is a metagenome based community structure explorer and primer evaluation tool. With a metagenome dataset input, MIPE demonstrates the detailed composition taxonomy information, and the coverage of the primer of interest.
MIPE contains three perl scripts.
MIPE_pre_program.pl does Step0: Pre-Propcessing. It uses BLAST tools to abstract target gene from metagenome data set. Metatranscriptome data can skip this step.
MIPE_main_program.pl does SSU taxonomy by mothur v1.33.3 and evaluates SSU primer binding sites and calculate primer coverage.
MIPE_main_program_metatranscriptome.pl does SSU and LSU taxonomy with mothur v1.33.3 and evaluates SSU primer binding sites and calculate primer coverage.
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Platform: Linux Installation: MIPE contains somes perl scripts. No need to install MIPE but you need to download MIPE dependences.
MIPE dependences downloading If you use the SILVA reference files you should be aware of their dual-use license https://www.arb-silva.de/silva-license-information
All MIPE files and dependences must be in the same directory. Copy mothur v1.33.3 into the working directory, then input:
$chmod 755 mothur
Download Silva.seed_v119.tgz from mothur website. I use mothue modified Silva reference files release 119 to build v119silva.SSU.fasta, v119silva.SSU_PICK.fasta and v119fangsilva.SSU.silva.tax .
$wget http://www.mothur.org/w/images/5/56/Silva.seed_v119.tgz
$tar xvzf Silva.seed_v119.tgz
$mv silva.seed_v119.align v119silva.SSU.fasta
$mv silva.seed_v119.tax v119fangsilva.SSU.silva.tax #I recommend you to change all parentheses for brackets.
$perl SILVA_ENLONG.pl #To build v119silva.SSU_PICK.fasta
Download SILVA_119_LSURef_tax_silva_full_align_trunc.fasta.gz from SILVA website. I clustered SILVA lSU database (v119) with Usearch (v5.2.32) at a 99% sequence identity level to decrease LSU database and made a taxonomy file (v119silva.LSU.silva.tax) for mothur.
$gunzip -c SILVA_119_LSURef_tax_silva_full_align_trunc.fasta.gz > SILVA_119_LSURef_tax_silva_full_align_trunc.fasta
$./mothur "#get.seqs(fasta=SILVA_119_LSURef_tax_silva_full_align_trunc.fasta,accnos=v119silva.LSU.silva.tax)"
$mv SILVA_119_LSURef_tax_silva_full_align_trunc.pick.fasta v119silva.LSU.fasta #######################################################################################################################################
Citing MIPE: Zou, B., Li, J., Zhou, Q., & Quan, Z. X. (2017). MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool. PloS one, 12(3), e0174609.