| ... | ... | @@ -4,6 +4,7 @@ title: Functional annotations |
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Functional annotation helps bringing biological meaning to genetic sequences. Functional annotation is usually obtained through protein sequence similarity. Indeed, across two organisms, if two sequences are very similar, one can infer that they can encode for the same biological function.
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There are several main parameters that will impact the process of functional annotation:
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- how distant is the species which was actually annotated with experimental data (the reference)
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| ... | ... | @@ -27,4 +28,17 @@ Then create the eggNOG database which contains ortholog groups and the functiona |
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Finally, the emapper program can be run to annotate each genome:
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`emapper.py --cpu 10 -i $input --output ${prefix}.tsv -m diamond --data_dir eggnog_db --database 33090` |
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\ No newline at end of file |
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`emapper.py --cpu 10 -i $input --output ${prefix}.tsv -m diamond --data_dir eggnog_db --database 33090`
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Here are the first line of the annotation file for _Medicago truncatula_:
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```
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## Mon Mar 21 17:38:09 2022
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## emapper-2.1.6-1910c4c
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## emapper.py --cpu 10 -i mtru.fa --output mtru -m diamond --data_dir eggnog_db --database euk
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##
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#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
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MtrunA17Chr2g0276741.1 3880.AES63119 0.0 2169.0 2CMVN@1|root,2QS81@2759|Eukaryota,37QCI@33090|Viridiplantae,3G9HZ@35493|Streptophyta,4JE84@91835|fabids 35493|Streptophyta S Methionine MMT GO:0001887,GO:0003674,GO:0003824,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0005829,GO:0006732,GO:0006790,GO:0008150,GO:0008152,GO:0008168,GO:0008757,GO:0009987,GO:0016740,GO:0016741,GO:0017144,GO:0032259,GO:0044237,GO:0044424,GO:0044444,GO:0044464,GO:0046500,GO:0051186,GO:0071704 2.1.1.12 ko:K08247 ko00450,map00450 - R04772 RC00003,RC01212 ko00000,ko00001,ko01000 - - - Aminotran_1_2,MTS,Methyltransf_31
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MtrunA17Chr2g0276751.1 3880.AES63120 0.0 1156.0 COG3104@1|root,KOG1237@2759|Eukaryota,37P3M@33090|Viridiplantae,3GBJZ@35493|Streptophyta,4JJBT@91835|fabids 35493|Streptophyta E Protein NRT1 PTR FAMILY 4.3-like - GO:0005575,GO:0005623,GO:0005886,GO:0008150,GO:0009605,GO:0009607,GO:0009624,GO:0016020,GO:0043207,GO:0044464,GO:0050896,GO:0051704,GO:0051707,GO:0071944 - ko:K14638 - - - - ko00000,ko02000 2.A.17.3 - - PTR2
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```
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