---
title: "Blast"
output: html_document
---

Blast is a common approach used throughout efforts. Here is a notebook to get you started with a test dataset. As part you will be writing to a directory named `big-stuff` this directory is ignored by git.


Blast will need to be installed on your local machine. 

## Download stand-alone blast (optional)
see ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
```{bash}
cd /Applications/bioinfo/
curl -O https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-x64-macosx.tar.gz
tar -xf ncbi-blast-2.12.0+-x64-macosx.tar.gz
cd -
```


## Set blast directory

```{bash}
bldir=/Applications/bioinfo/ncbi-blast-2.12.0+/bin/
#run blastx help to test 
${bldir}blastx -h
```

## Create blast database (protein)

Check release at https://www.uniprot.org/downloads. For example the release used here is **r2021_04**

```{bash}
cd ../big-stuff
curl -O https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
mv uniprot_sprot.fasta.gz uniprot_sprot_r2021_04.fasta.gz
gunzip -k uniprot_sprot_r2021_04.fasta.gz
cd -
```


```{bash}
#will need to re assign bldir
bldir=/Applications/bioinfo/ncbi-blast-2.12.0+/bin/

${bldir}makeblastdb \
-in ../big-stuff/uniprot_sprot_r2021_04.fasta \
-dbtype prot \
-out ../big-stuff/uniprot_sprot_r2021_04
```


```{bash}

#will need to re assign bldir
bldir=/Applications/bioinfo/ncbi-blast-2.12.0+/bin/


${bldir}blastx \
-query ../data/tutorial/Ab_4denovo_CLC6_a.fa \
-db ../big-stuff/uniprot_sprot_r2021_04 \
-out ../analyses/tutorial/Ab_4-uniprot_blastx.tab \
-evalue 1E-20 \
-num_threads 8 \
-max_target_seqs 1 \
-outfmt 6
```

```{bash}
head -3 ../analyses/tutorial/Ab_4-uniprot_blastx.tab
```

