Layers/Functional-annotations.md

@@ -13,6 +13,7 @@ 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)
@@ -149,6 +150,23 @@ md5sum -c interproscan-5.65-97.0-bit.tar.gz.md5
 
 ./interproscan-5.65-97.0/interproscan.sh -cpu 15 -iprlookup -goterms -f TSV -i mtrun.fa -o mtru.tsv
 ```
+In case of error, using a docker container can be a solution.
+```
+docker pull interpro/interproscan:5.65-97.0
+docker run --rm \
+    -v $PWD/interproscan-5.65-97.0/data:/opt/interproscan/data \ # mount the data dir of interproscan
+    -v $PWD/input:/input \ # mount the input local dir containing the protein files
+    -v $PWD/results:/output \
+    -v $PWD/temp:/temp \
+    interpro/interproscan:5.65-97.0 \
+    --input /input/proteins/mtrun_prot.fa \
+    --disable-precalc \
+    --output-dir /output \
+    --tempdir /temp \
+    --cpu 50
+```
+
+The output annotation file has the following format:
 ```
 MtrunA17Chr2g0319311.1  45cf42d1c723e145a264cdb6d0420efe        541     Pfam    PF01501 Glycosyl transferase family 8   218     515     1.1E-84 T       17-08-2022      IPR002495       Glycosyl transferase
 , family 8      GO:0016757