fetch‐eggnog‐hmmer‐db

Downloads Profile HMM database for the specified taxon.

For the full description of the action's inputs, outputs and parameters run qiime moshpit fetch-eggnog-hmmer-db --help in the terminal.

Inputs

None.

Parameters

• taxon-id (int): Taxon ID number.

Outputs

• idmap (EggnogHmmerIdmap % Properties('eggnog')): List of protein families in hmm-db.
• hmm-db (ProfileHMM[MultipleProtein] % Properties('eggnog')): Collection of Profile HMMs.
• pressed-hmm-db (ProfileHMM[PressedProtein] % Properties('eggnog')): Collection of Profile HMMs in binary format and indexed.
• fastas (GenomeData[Proteins] % Properties('eggnog')): Seed alignments for the protein families in hmm-db.

Citation

@article{key0,
 author = {Huerta-Cepas, Jaime and Szklarczyk, Damian and Heller, Davide and Hernández-Plaza, Ana and Forslund, Sofia K and Cook, Helen and Mende, Daniel R and Letunic, Ivica and Rattei, Thomas and Jensen, Lars J and von Mering, Christian and Bork, Peer},
 doi = {10.1093/nar/gky1085},
 issn = {0305-1048},
 journal = {Nucleic Acids Research},
 month = {January},
 number = {D1},
 pages = {D309--D314},
 shorttitle = {eggNOG 5.0},
 title = {eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses},
 url = {https://doi.org/10.1093/nar/gky1085},
 urldate = {2024-01-18},
 volume = {47},
 year = {2019}
}

@misc{key1,
 title = {HMMER},
 url = {http://hmmer.org/},
 urldate = {2024-05-22}
}