---
title: "16-BLAST-pisaster"
output: html_document
date: "2025-03-12"
---
Rmd to run BLAST on _P. ochraceus_ genome to annotate it. 

Will use the example code provided at [Roberts Lab - resources - bio-Annotation](https://robertslab.github.io/resources/bio-Annotation/)

Specifically: [https://robertslab.github.io/tusk/modules/04-blast.html](https://robertslab.github.io/tusk/modules/04-blast.html) 

The genome fasta lives:  
`../data/jordan-uni3279-mb-hirise-slc3v_06-07-2022_final_assembly.fasta`

```{r}
library(Biostrings)
library(reshape2)
```

# Create Database
```{r}
current_time <- format(Sys.time(), "%B %d, %Y %H:%M:%S")
cat("current date and time is ", current_time)
```

```{bash}
pwd
```

this has been done in 15-BLAST-pycno.Rmd
```{bash}
#cd ../data
#curl -O https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
#mv uniprot_sprot.fasta.gz uniprot_sprot_r2023_04.fasta.gz
#gunzip -k uniprot_sprot_r2023_04.fasta.gz
```

this has also been done in 15-BLAST-pycno.Rmd
make the database
```{bash}
#mkdir ../blastdb
#/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
#-in ../data/uniprot_sprot_r2023_04.fasta \
#-dbtype prot \
#-out ../blastdb/uniprot_sprot_r2023_01
```

# Query Fasta File
as noted above, it lives: `../data/jordan-uni3279-mb-hirise-slc3v__06-07-2022__final_assembly.fasta`

```{bash}
head -3 ../data/jordan-uni3279-mb-hirise-slc3v__06-07-2022__final_assembly.fasta
```

```{bash}
echo "How many sequences are there?"
grep -c ">" ../data/jordan-uni3279-mb-hirise-slc3v__06-07-2022__final_assembly.fasta
```
What? only 122?