tldr:

Got GO annotations for Deep Dive Protein sets:

https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/output/20-Apul-gene-annotation/Apul-protein-GO.tsv

https://raw.githubusercontent.com/urol-e5/deep-dive/main/E-Peve/output/20-Peve-gene-annotation/Peve-protein-GO.tsv

https://github.com/urol-e5/deep-dive/raw/main/F-Pmea/output/20-Pmea-gene-annotation/Pmea-protein-GO.tsv

Here is example code

20-Apul Annotation

Steven Roberts 25 August, 2024

Apul

Protein

cd ../data

curl -O https://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1.protein.faa

head ../data/GCF_013753865.1_Amil_v2.1.protein.faa

ls ../../data/blast_dbs

Swiss Prot download

cd ../../data/blast_dbs
curl -O https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
mv uniprot_sprot.fasta.gz uniprot_sprot_r2024_04.fasta.gz
gunzip -k uniprot_sprot_r2024_04.fasta.gz

head ../../data/blast_dbs/uniprot_sprot_r2024_04.fasta
echo "Number of Sequences"
grep -c ">" ../../data/blast_dbs/uniprot_sprot_r2024_04.fasta

/home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \
-in ../../data/blast_dbs/uniprot_sprot_r2024_04.fasta \
-dbtype prot \
-out ../../data/blast_dbs/uniprot_sprot_r2024_04

Blastp

fasta="../data/GCF_013753865.1_Amil_v2.1.protein.faa"

/home/shared/ncbi-blast-2.15.0+/bin/blastp \
-query $fasta \
-db ../../data/blast_dbs/uniprot_sprot_r2024_04 \
-out ../output/20-Apul-gene-annotation/blastp_out.tab \
-evalue 1E-05 \
-num_threads 48 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

wc -l ../output/20-Apul-gene-annotation/blastp_out.tab

tr '|' '\t' < ../output/20-Apul-gene-annotation/blastp_out.tab \
> ../output/20-Apul-gene-annotation/blastp_out_sep.tab

head -1 ../output/20-Apul-gene-annotation/blastp_out_sep.tab

Download GO info

sr320@raven:/home/shared/8TB_HDD_01/sr320/github/deep-dive/data$ curl -H "Accept: text/plain; format=tsv" "https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Creviewed%2Cid%2Cprotein_name%2Cgene_names%2Corganism_name%2Clength%2Cgo_p%2Cgo_c%2Cgo%2Cgo_f%2Cgo_id&format=tsv&query=%28*%29+AND+%28reviewed%3Atrue%29" -o SwissProt-Annot-GO_082324.tsv

wc -l ../../data/SwissProt-Annot-GO_082324.tsv

Join blast with GO info

bltabl <- read.csv("../output/20-Apul-gene-annotation/blastp_out_sep.tab", sep = '\t', header = FALSE)

spgo <- read.csv("../../data/SwissProt-Annot-GO_082324.tsv", sep = '\t', header = TRUE)

annot_tab <- left_join(bltabl, spgo, by = c("V3" = "Entry")) %>%
  select(
    query = V1,
    blast_hit = V3,
    evalue = V13,
    ProteinNames = Protein.names,
    BiologicalProcess = Gene.Ontology..biological.process.,
    GeneOntologyIDs = Gene.Ontology.IDs
  )

head(annot_tab)

write.table(annot_tab, 
            file = "../output/20-Apul-gene-annotation/Apul-protein-GO.tsv", 
            sep = "\t", 
            row.names = FALSE, 
            quote = FALSE)

head ../output/20-Apul-gene-annotation/Apul-protein-GO.tsv

Actual code at

https://github.com/urol-e5/deep-dive/blob/main/D-Apul/code/20-Apul-gene-annotation.Rmd

https://github.com/urol-e5/deep-dive/blob/main/E-Peve/code/20-Peve-gene-annotation.Rmd

https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/code/20-Pmea-gene-annotation.Rmd

--- title: "Git that Pro GO" description: "Deep dive Protein Annotation" categories: [blast, e5] #citation: date: 08-25-2024 image: http://gannet.fish.washington.edu/seashell/snaps/Monosnap__in_UniProtKB_search_571864__UniProt_2024-08-23_16-18-03.png # finding a good image author: - name: Steven Roberts url: orcid: 0000-0001-8302-1138 affiliation: Professor, UW - School of Aquatic and Fishery Sciences affiliation-url: https://robertslab.info #url: # self-defined draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready! format: html: code-fold: FALSE code-tools: true code-copy: true highlight-style: github code-overflow: wrap --- ```{r setup, include=FALSE} knitr::opts_chunk$set( echo = TRUE, # Display code chunks eval = FALSE, # Evaluate code chunks warning = FALSE, # Hide warnings message = FALSE, # Hide messages fig.width = 6, # Set plot width in inches fig.height = 4, # Set plot height in inches fig.align = "center", # Align plots to the center comment = "" # Prevents appending '##' to beginning of lines in code analyses ) ``` tldr: Got GO annotations for Deep Dive Protein sets: https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/output/20-Apul-gene-annotation/Apul-protein-GO.tsv https://raw.githubusercontent.com/urol-e5/deep-dive/main/E-Peve/output/20-Peve-gene-annotation/Peve-protein-GO.tsv https://github.com/urol-e5/deep-dive/raw/main/F-Pmea/output/20-Pmea-gene-annotation/Pmea-protein-GO.tsv --- Here is example code 20-Apul Annotation ================ Steven Roberts 25 August, 2024 Apul # Protein ``` bash cd ../data curl -O https://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1.protein.faa ``` ``` bash head ../data/GCF_013753865.1_Amil_v2.1.protein.faa ``` ``` bash ls ../../data/blast_dbs ``` # Swiss Prot download ``` bash cd ../../data/blast_dbs curl -O https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz mv uniprot_sprot.fasta.gz uniprot_sprot_r2024_04.fasta.gz gunzip -k uniprot_sprot_r2024_04.fasta.gz ``` ``` bash head ../../data/blast_dbs/uniprot_sprot_r2024_04.fasta echo "Number of Sequences" grep -c ">" ../../data/blast_dbs/uniprot_sprot_r2024_04.fasta ``` ``` bash /home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \ -in ../../data/blast_dbs/uniprot_sprot_r2024_04.fasta \ -dbtype prot \ -out ../../data/blast_dbs/uniprot_sprot_r2024_04 ``` # Blastp ``` bash fasta="../data/GCF_013753865.1_Amil_v2.1.protein.faa" /home/shared/ncbi-blast-2.15.0+/bin/blastp \ -query $fasta \ -db ../../data/blast_dbs/uniprot_sprot_r2024_04 \ -out ../output/20-Apul-gene-annotation/blastp_out.tab \ -evalue 1E-05 \ -num_threads 48 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt 6 ``` ``` bash wc -l ../output/20-Apul-gene-annotation/blastp_out.tab ``` ``` bash tr '|' '\t' < ../output/20-Apul-gene-annotation/blastp_out.tab \ > ../output/20-Apul-gene-annotation/blastp_out_sep.tab head -1 ../output/20-Apul-gene-annotation/blastp_out_sep.tab ``` # Download GO info ![](http://gannet.fish.washington.edu/seashell/snaps/Monosnap__in_UniProtKB_search_571864__UniProt_2024-08-23_16-18-03.png) sr320@raven:/home/shared/8TB_HDD_01/sr320/github/deep-dive/data$ curl -H "Accept: text/plain; format=tsv" "https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Creviewed%2Cid%2Cprotein_name%2Cgene_names%2Corganism_name%2Clength%2Cgo_p%2Cgo_c%2Cgo%2Cgo_f%2Cgo_id&format=tsv&query=%28*%29+AND+%28reviewed%3Atrue%29" -o SwissProt-Annot-GO_082324.tsv ``` bash wc -l ../../data/SwissProt-Annot-GO_082324.tsv ``` # **Join blast with GO info** ``` r bltabl <- read.csv("../output/20-Apul-gene-annotation/blastp_out_sep.tab", sep = '\t', header = FALSE) spgo <- read.csv("../../data/SwissProt-Annot-GO_082324.tsv", sep = '\t', header = TRUE) ``` ``` r annot_tab <- left_join(bltabl, spgo, by = c("V3" = "Entry")) %>% select( query = V1, blast_hit = V3, evalue = V13, ProteinNames = Protein.names, BiologicalProcess = Gene.Ontology..biological.process., GeneOntologyIDs = Gene.Ontology.IDs ) ``` ``` r head(annot_tab) ``` ``` r write.table(annot_tab, file = "../output/20-Apul-gene-annotation/Apul-protein-GO.tsv", sep = "\t", row.names = FALSE, quote = FALSE) ``` ``` bash head ../output/20-Apul-gene-annotation/Apul-protein-GO.tsv ``` --- Actual code at https://github.com/urol-e5/deep-dive/blob/main/D-Apul/code/20-Apul-gene-annotation.Rmd https://github.com/urol-e5/deep-dive/blob/main/E-Peve/code/20-Peve-gene-annotation.Rmd https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/code/20-Pmea-gene-annotation.Rmd