介绍
**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.
Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence).
Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb).
EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de
# Documentation
https://github.com/jhcepas/eggnog-mapper/wiki
If you use this software, please cite:
[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain
prediction at the metagenomic scale. Carlos P. Cantalapiedra,
Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293
[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
orthology resource based on 5090 organisms and 2502 viruses. Jaime
Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia
K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars
J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8;
47(Database issue): D309–D314. doi: 10.1093/nar/gky1085
输入
基因的蛋白序列文件（fasta格式）
例如：
>geneName1
MKLLAHILCLSLALAWAQSQDHALAVLDRCEGLEMDAVAVNEEGIPYFFKGDHLFKGFHG
>geneName2
MWVGEERFEGSRLVVVTRGAVSVGGEGVEDVGGGAVWGLVRSAQSEHPGRFVLVDADVDA
DVDTGVVPDVVGLGESQVAVRGGRVWVPRLVGVNSGGGVRAGGGVVRRGLGSGVALVTGG
TGLLGGLVARHLVSAYGVGELVLVSRRGPGAPGVGALVGELEELGAGVRVVACDVADRGA
VAELVGSIEGLRVVVHAAGAVDDGVIGSLDGGRLRGVMGPKAWGAWHLHELTSGLDLS
结果
注释的结果表格文件
格式例如：
#query seed_ortholog evalue score eggNOG_OGs max_annot_lvl COG_category Description Preferred_name GOs EC KEGG_ko KEGG_Pathway
KEGG_Module KEGG_Reaction KEGG_rclass BRITE KEGG_TC CAZy BiGG_Reaction PFAMs
geneName3 494419.ALPM01000100_gene1074 4.15e-05 48.9 COG0747@1|root,COG0747@2|Bacteria,2GM5G@201174|Actinobacteria 201174|Actinobacteria
E ABC transporter substrate-binding protein - - - ko:K02035 ko02024,map02024 M00239 - - ko00000,ko
00001,ko00002,ko02000 3.A.1.5 - - SBP_bac_5
