| ... | ... | @@ -5,6 +5,7 @@ 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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| ... | ... | @@ -14,10 +15,12 @@ There are several main parameters that will impact the process of functional ann |
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Several tools to functionally annotate sequences exist. They do not all require the same input, nor will they deliver the same output, and are therefore complementary.
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# Requirements
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In Ortho_KB, we integrate functional annotation from EggNOG, MapMan, TRAPID and InterPro.
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In Ortho_KB, we integrate functional annotation from EggNOG, MapMan, InterPro and TRAPID.
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## EggNOG
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The annotation tool EggNOG-mapper (https://github.com/eggnogdb/eggnog-mapper) relies on EggNOG databases to annotate genes with knowledge from orthologs on other genomes.
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First, install emapper, which can be done for example with conda:
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`conda create -n emapper -c bioconda eggnog-mapper`
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| ... | ... | @@ -41,4 +44,17 @@ Here are the first line of the annotation file for _Medicago truncatula_: |
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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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The EggNOG-mapper output file includes several categories of annotation, including Gene Ontology (GO) annotation, Kegg Ontology (KO) annotation, PFAM annotations etc. In the case of Ortho_KB, only the Description and Preferred_name fields are currently integrated.
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## MapMan
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## TRAPID
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The **online** annotation tool TRAPID (https://bioinformatics.psb.ugent.be/trapid_02/documentation/general) has been designed to annotate RNA-seq transcriptome experiments. It relies on the PLAZA database (https://bioinformatics.psb.ugent.be/plaza/), which contains plant genomic data. TRAPID can be also used to annotate genomes. The process is the following:
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1. Create an account (`Register` on the top-right side)
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2. In Experiment overview, click on `ADD NEW EXPERIMENT`
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3. Name it and select `PLAZA 4.5 dicots` (or above) as the `Reference database`
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4. Click on the new experiment name
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5. Click on `Import data` on the left-side panel
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6. |
