Layers/Functional-annotations.md

@@ -7,6 +7,7 @@ title: Functional annotations
 
 
 
+
 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.
 There are several main parameters that will impact the process of functional annotation:
 - how distant is the species which was actually annotated with experimental data (the reference)
@@ -49,20 +50,31 @@ The EggNOG-mapper output file includes several categories of annotation, includi
 
 ## MapMan
 
+The online annotation tool Mercator4 ([https://www.plabipd.de/mercator_main.html](https://www.plabipd.de/mercator_main.html)) annotate sequences with the MapMan ontology. This ontology is characterized by synthetic descriptors of gene functions. A gene is usually associated to one to two MapMan bins (= terms).
+MapMan requires DNA or protein input (we use the latter which can provide more annotations).
+
+![mapman](uploads/7f00c2fbc9050028dd349d3dc815e82d/image.png)
+
+The annotation should be done after about 10min.
+
+
 ## TRAPID
 
-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:
+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, by providing it with CDS sequences. The process is the following:
 
 1. Create an account (`Register` on the top-right side)
 2. In Experiment overview, click on `ADD NEW EXPERIMENT`
 3. Name it and select `PLAZA 4.5 dicots` (or above) as the `Reference database`
 4. Click on the new experiment name
 5. Click on `Import data` on the left-side panel
-6. Add your transcript file (can be .gzip)
+6. Add your transcript file (can be .gzip if large)
 7. Click on `ADD FILE / URL`
 8. Click on `LOAD DATA INTO DATABASE`
 9. Wait for the Status to switch from `loading_db` to `upload`
 10. Check the number of processed transcripts
 11. Click on `PROCESS TRANSCRIPTS`
 ![process_transcripts](uploads/9025b099e10cacfacfc62f3c8ae56230/image.png)
+Perform as depicted on the picture above.
 14. Wait for the Status to switch from `processing` to `finished`
+ (it can take a few hours)
+15. 
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