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Update Functional annotations authored by Baptiste Imbert's avatar Baptiste Imbert
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Layers/Functional-annotations.md
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......@@ -12,6 +12,7 @@ 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)
......@@ -60,7 +61,7 @@ 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 a protein or DNA input (we use the latter which can provide more annotations, providing CDS files).
MapMan requires a protein or DNA input (we provide a **FASTA of CDS**, using the DNA input which can provide more annotations).
![mapman](uploads/7e77a56c79e04630ac6cf69ae7912aaa/image.png)
......@@ -79,7 +80,7 @@ Bins are listed with the genes which are annotated with them. The structure of t
## 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, by providing it with CDS sequences. 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 a **FASTA of 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`
......@@ -133,7 +134,7 @@ _Note 2: TRAPID is no longer actively updated. Other options will be considered_
## InterPro
InterPro is a database which includes a range of sources for the annotation of protein function. InterProScan allows to scan InterPro for the submitted protein sequences (FASTA) and retrieve associated annotations.
InterPro is a database which includes a range of sources for the annotation of protein function. InterProScan allows to scan InterPro for the submitted **FASTA of protein** sequences and retrieve associated annotations.
Please check https://interproscan-docs.readthedocs.io/en/latest/HowToDownload.html for the links to download the latest version of InterProScan.
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