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Metagenomic HMM metabolic profiling

Subcategory: molecular
Papers: 2 | Mentions: 4

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Description

Comprehensive Hidden Markov Model analysis of metagenomic sequences to identify and quantify metabolic functions across biogeochemical pathways. Uses both standardized TIGR-FAM and custom HMM databases with specific cutoff scores for gene identification.

Typical Equipment

  • TIGR-FAM database
  • Custom HMM databases

Output Measurements

  • metabolic gene abundance
  • functional diversity
  • biogeochemical pathway representation

Papers Using This Protocol (2)

article

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

2021Microbiomeusing
article

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

2019Ecology and Evolutionusing

Species Studied With This Protocol

Nitrososphaera sp.

1 paper

Desulfobacca acetoxidans

Syntrophaceae1 paper

Geobacter spp.

1 paper

Desulfuromonas sp.

1 paper

Thaumarchaeota

1 paper

Bathyarchaeota

1 paper

Euryarchaeota

1 paper

Alphaproteobacteria

1 paper

Gammaproteobacteria

1 paper

Shewanella oneidensis

1 paper

Places Where Used

Colorado River

stream1 paper

Gunnison

study site1 paper

Gunnison River Basin

watershed1 paper

Crested Butte

study site1 paper

Boulder

region1 paper

south-central Colorado

region1 paper

San Joaquin Valley

valley1 paper

Uncompahgre River Basins

watershed1 paper

eastern Tibetan plateau

region1 paper

PLM

study site1 paper