MIPE specifications

Information


Unique identifier OMICS_17118
Name MIPE
Alternative name MIcrobiota Prior knowledge Explorer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Zhe-Xue Quan

Publication for MIcrobiota Prior knowledge Explorer

MIPE citations

 (2)
library_books

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method

2018
Front Microbiol
PMCID: 5797801
PMID: 29445367
DOI: 10.3389/fmicb.2018.00093

[…] with any ambiguous nucleotide and homopolymer length >8 bases were removed from the assembled sequences in mothur v1.33.3.For each metatranscriptome (MT) dataset, sequences >250 bp were submitted to MIPE software for identification of archaeal, bacterial, and eukaryotic SSU rRNA (denoted as “MT-SSU”), with a bootstrap cut-off of 80% against the SILVA SSU seed v119 database. Identified prokaryotic […]

library_books

Modified RNA seq method for microbial community and diversity analysis using rRNA in different types of environmental samples

2017
PLoS One
PMCID: 5634646
PMID: 29016661
DOI: 10.1371/journal.pone.0186161

[…] sly proposed [].To correctly assign all SSU rRNA reads within the RNA-seq datasets of the environmental samples, sequences longer than 250 bp were classified against the SILVA SSURef v119 database in MIPE (https://github.com/zoubinok/MIPE) with a bootstrap cut-off of 80%, and sequences that were identified as chloroplast, mitochondria or human were removed. Mismatches of the utilized primer 8F (5’ […]

MIPE institution(s)
Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China; Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
MIPE funding source(s)
This work was supported by the National Natural Science Foundation of China (31170114).

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