102
Functional annotation, 41
Functional profiling, 68
G
Gene calling, 43
General-Error-Model based Simulators, 69
Genomes-OnLine-Database (GOLD), 44
Genomic and proteomic analysis, 4
GeoChip 3.0 microarray technology, 32
Global Ocean Sample (GOS), 43
Glomalin, 15
Greenhouse gas emissions, 4
H
Hexachlorocyclohexane (HCH), 29
Hidden Markov-Model (HMM), 43
High-throughput sequencing technologies,
46–47
Horseradish peroxidase (HRP) enzyme, 25
HUMAnN, 68
I
IDBA-UD, 69
Induced systemic resistance (ISR), 73
INDUS, 66
Interpolated-Markov-Model (IMM), 43
K
KeggMapper tool, 46, 48
Kyoto-Encyclopedia, 44
L
LefSe, 68
Lowest common ancestor (LCA), 67
M
Marginal lands, 15
MARTA, 66
Metabolic pathways, 68
MetaCluster, 66
MetaGeneAnnotator (MGA), 65
Metagenomic approaches
applications, 48
data mining approaches, 47
EBI, 44
ecosystems, 39
gene finding and comparative, 41
interlinking soil, 49
microbial communities, 39
phylogenetic analysis, 42
rRNA gene, 39
Metagenomic data, 39, 45
Metagenomic dataset, 47
Metagenomics, 40
and metatranscriptomics, 55
Metagenomics data analysis
AMPHORA, 45
assembly, 41
community-level analysis, 44
comparing pathways, 46
computational biology, 46
DNA, 46
EBI, 44
gene calling, 43
high-throughput techniques, 41
MEGAN, 45
MG-RAST, 44
NGS data, 42
phylogenetic analysis, 42
sequence binning, 42
taxonomic binning, 42
Meta-IDBA toolkit, 65
MetaPhlAn, 66
MetaPhyler, 67
METAREP, 70
metaSHARK, 68
MetaSim, 69
Metastats, 68
Metatranscriptomics
applications, 60
biochemical approaches, 57
biological interpretation, 54
characterization, 56
deep sequencing, 54
differential gene expression, 53
DNA extraction, 56
environmental conditions, 57
functional data, 52
microbial biomass, 59
mRNA, 51, 53
probe application, 53
proteomics, 55
RNA-seq reads, 53
soil environment, 59
2-D gel electrophoresis, 56
Metatranscriptomics data analysis, 61
MG-RAST, 70
Microbial communities, 4
Microbial community structure, 24–26, 28
Microbial diversity, 2
Index