Results Interpretation

Jaime Huerta-Cepas edited this page Nov 6, 2017 · 8 revisions

[project_name].emapper.hmm_hits file

For each query sequence, a list of significant hits to eggNOG Orthologous Groups (OGs) is reported. Each line in the file represents a hit, where evalue, bit-score, query-coverage and the sequence coordinates of the match are reported. If multiple hits exist for a given query, results are sorted by e-value.

[project_name].emapper.seed_orthologs file

each line in the file provides the best match of each query within the best Orthologous Group (OG) reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. If using the diamond search mode, seed orthologs are directly obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.

[project_name].emapper.annotations file

This file provides final annotations of each query. Tab-delimited columns in the file are:

  1. query_name: query sequence name
  2. seed_eggNOG_ortholog: best protein match in eggNOG
  3. seed_ortholog_evalue: best protein match (e-value)
  4. seed_ortholog_score: best protein match (bit-score)
  5. predicted_gene_name: Predicted gene name for query sequences
  6. GO_terms: Comma delimited list of predicted Gene Ontology terms
  7. KEGG_KO: Comma delimited list of predicted KEGG KOs
  8. BiGG_Reactions: Comma delimited list of predicted BiGG metabolic reactions
  9. Annotation_tax_scope: The taxonomic scope used to annotate this query sequence
  10. Matching_OGs: Comma delimited list of matching eggNOG Orthologous Groups
  11. best_OG|evalue|score: Best matching Orthologous Groups (only in HMM mode)
  12. COG functional categories: COG functional category inferred from best matching OG
  13. eggNOG_HMM_model_annotation: eggNOG functional description inferred from best matching OG
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