eggnog‐hmmer‐search - bokulich-lab/q2-annotate GitHub Wiki

Find homolog sequences in contigs or MAGs against a HMMER reference database.

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

Inputs

sequences (SampleData[Contigs] | FeatureData[MAG]): MAGs or contigs to search for homolog sequences against a Diamond database.
idmap (EggnogHmmerIdmap % Properties('eggnog')): List of protein families in hmm-db.
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.

Outputs

eggnog-hits (SampleData[BLAST6]): Predicted hits. For each FASTA file in the input, a table is generated where every row is a hit (a predicted homolog) and columns are information about that specific hit/alignment. These tables or table, depending on whether there are multiple fasta files in the input, are all contained in this output artifact. For more information about these tables take a look at the Diamond documentation.
table (FeatureTable[Frequency]): Feature table with counts of orthologs per sample/MAG.

Example Use

qiime moshpit eggnog-hmmer-search \
   --i-fastas hmmr_db_2/fastas.qza \
   --i-idmap hmmr_db_2/idmap.qza \
   --i-pressed-hmm-db hmmr_db_2/pressed_hmm_db.qza \
   --i-sequences mags.qza \
   --o-eggnog-hits hits.qza \
   --o-table table.qza \
   --p-num-partitions 4 \
   --parallel \
   --verbose

Tutorials

List of tutorials that involve this action.

Functional Annotation of MAGs (or Contigs)

Links to Relevant Resources

Citation

@misc{key0,
 title = {HMMER},
 url = {http://hmmer.org/},
 urldate = {2024-05-22}
}

@article{key1,
 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}
}