blast_commands.md

BLAST++

Basic Local Alignment Search Tool: basic usage

Blast remote

Blast remote is a very usefull commands because allows to connect to GenBank to serch on their most recent databases, withouth the need to have a database locally. Consider that uses sftp to connect remotely to the GenBank database, so it could get slower.

# BLASTn nucleotide search on nucleotides database
blastn -query FILE.fasta -remote -db nr -out contigs_blastx        
# BLASTx nucleotide search on proteins database
blastx -query FILE.fasta -remote -db nr -out contigs_blastx        
# BLASTp protein sequence search on protein database
blastx -query FILE.fasta -remote -db nr -out contigs_blastx        

Blast all uses a flag to indicate the search

blastall -i FILE.fasta -d DATABASE.local -p blastn -o out_contigs_blast.txt -a 6

BLASTn nucleotide vs nucleotides

blastn -query LS12-703-506_k64ml-contigs.fa -db /home/administrator/vDB/pvirusDB/pvirusDB -out LS12-703-506_k64ml-contigs_blastn  -num_threads 4 

BLASTx nuelcotide vs aminoacids

blastx -query LS12-701-503_ak64-contigs.fa -db /home/administrator/vDB/U95/plant_206_U95/U95Prot/vU95prot -out  LS12-701-503_ak64-contigs_blastx_vU95 -num_threads 4  

Creating databases

Blast database\

makeblastdb -in Viral_nucleic_acid_database -out virusDB -dbtype nucl -hash_index

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Tutorial

BLast analysis
blastall -i filename_input.fa -d virusDB -p blastn -o filename_ouput.txt -m 5 -a 4\

Notes:
-i refers to the input file
-d refers to the DataBase
-p refers to the program to use in this case blastn
-o refers to the output name
-m refers to the output format (see formats http://tinyurl.com/mhpzc3v)
-a refers to the number of threads to use
-F dust refers to avoid Karlin-Altschul parameter.

blast loops

An example searching over multiple files $./multi_blast.sh

for k in {20..40}; 
do
	blastall -i Grassy_contigs-k$k.fa -d vir_oidDB -p blastn -o grassy_blast_k$k.fa -a 6
done