Local BLAST

Run BLAST searches locally using NCBI BLAST+ command-line tools.

Installation

# macOS
brew install blast

# Ubuntu/Debian
sudo apt install ncbi-blast+

# conda
conda install -c bioconda blast

# Verify installation
blastn -version

BLAST+ Programs

blastn

blastp

blastx

tblastn

tblastx

makeblastdb

Creating BLAST Databases

makeblastdb - Create Database

# Create nucleotide database
makeblastdb -in sequences.fasta -dbtype nucl -out my_db

# Create protein database
makeblastdb -in proteins.fasta -dbtype prot -out my_proteins

# With title and parse sequence IDs
makeblastdb -in sequences.fasta -dbtype nucl -out my_db \
    -title "My Reference Database" -parse_seqids

Key Options:

-in

-dbtype

nucl

prot

-out

-title

-parse_seqids

-taxid

-taxid_map

Database Files Created

my_db.nhr  # Header file (nucl) / .phr (prot)
my_db.nin  # Index file (nucl) / .pin (prot)
my_db.nsq  # Sequence file (nucl) / .psq (prot)
my_db.ndb  # Alias file (optional)
my_db.not  # ID index (if parse_seqids)
my_db.ntf  # Index (if parse_seqids)
my_db.nto  # Index (if parse_seqids)

Running BLAST Searches

Basic Usage

# BLASTN
blastn -query query.fasta -db my_db -out results.txt

# BLASTP
blastp -query proteins.fasta -db my_proteins -out results.txt

# BLASTX (translate query, search protein DB)
blastx -query genes.fasta -db nr -out results.txt

Common Options

-query

-query seq.fa

-db

-db nt

-out

-out results.txt

-outfmt

-outfmt 6

-evalue

-evalue 1e-5

-num_threads

-num_threads 8

-max_target_seqs

-max_target_seqs 100

-max_hsps

-max_hsps 1

-word_size

-word_size 11

-dust

-dust yes

-seg

-seg yes

Output Formats (-outfmt)

0

1

5

6

7

10

Tabular Output Fields (-outfmt 6)

Default columns:

qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

Custom columns:

blastn -query query.fa -db my_db -outfmt "6 qseqid sseqid pident length evalue stitle"

Available Fields:

qseqid

sseqid

pident

length

mismatch

gapopen

qstart

qend

sstart

send

evalue

bitscore

stitle

qcovs

qcovhsp

Code Patterns

Create Database and Search

#!/bin/bash
# Create database from reference sequences
makeblastdb -in reference.fasta -dbtype nucl -out ref_db -parse_seqids

# Run BLAST
blastn -query query.fasta -db ref_db -out results.txt \
    -outfmt 6 -evalue 1e-10 -num_threads 4

# View results
head results.txt

BLAST with Tabular Output

#!/bin/bash
blastn -query query.fasta -db my_db \
    -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle" \
    -evalue 1e-5 \
    -max_target_seqs 10 \
    -num_threads 8 \
    -out results.tsv

Filter and Sort Results

# Get hits with >90% identity
awk -F'\t' '$3 >= 90' results.tsv

# Sort by E-value
sort -t$'\t' -k11 -g results.tsv

# Get best hit per query
sort -t$'\t' -k1,1 -k11,11g results.tsv | sort -t$'\t' -k1,1 -u

Batch BLAST Multiple Files

#!/bin/bash
for query_file in queries/*.fasta; do
    base=$(basename "$query_file" .fasta)
    echo "Processing $base..."

    blastn -query "$query_file" -db my_db \
        -outfmt 6 -evalue 1e-5 -num_threads 4 \
        -out "results/${base}_blast.tsv"
done

Python Wrapper

import subprocess
import os

def make_blast_db(fasta_file, db_name, db_type='nucl'):
    cmd = ['makeblastdb', '-in', fasta_file, '-dbtype', db_type, '-out', db_name, '-parse_seqids']
    subprocess.run(cmd, check=True)

def run_blast(query, db, output, program='blastn', evalue=1e-5, threads=4, outfmt=6):
    cmd = [program, '-query', query, '-db', db, '-out', output,
           '-outfmt', str(outfmt), '-evalue', str(evalue), '-num_threads', str(threads)]
    subprocess.run(cmd, check=True)

def parse_blast_tabular(filename):
    columns = ['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen',
               'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore']
    hits = []
    with open(filename) as f:
        for line in f:
            values = line.strip().split('\t')
            hit = dict(zip(columns, values))
            hit['pident'] = float(hit['pident'])
            hit['evalue'] = float(hit['evalue'])
            hit['length'] = int(hit['length'])
            hits.append(hit)
    return hits

# Example usage
make_blast_db('reference.fasta', 'ref_db')
run_blast('query.fasta', 'ref_db', 'results.tsv')
hits = parse_blast_tabular('results.tsv')
for hit in hits[:5]:
    print(f"{hit['qseqid']} -> {hit['sseqid']}: {hit['pident']}% identity, E={hit['evalue']}")

Reciprocal Best BLAST

#!/bin/bash
# Forward BLAST: A vs B
blastp -query species_A.fasta -db species_B_db -outfmt 6 -evalue 1e-5 \
    -max_target_seqs 1 -out A_vs_B.tsv

# Reverse BLAST: B vs A
blastp -query species_B.fasta -db species_A_db -outfmt 6 -evalue 1e-5 \
    -max_target_seqs 1 -out B_vs_A.tsv

# Find reciprocal best hits
awk 'NR==FNR {a[$1]=$2; next} $2 in a && a[$2]==$1' A_vs_B.tsv B_vs_A.tsv

Extract Hit Sequences

# Get subject sequence by ID (requires -parse_seqids)
blastdbcmd -db my_db -entry "sequence_id" -out hit.fasta

# Get multiple sequences
blastdbcmd -db my_db -entry_batch ids.txt -out hits.fasta

# Get all sequences from database
blastdbcmd -db my_db -entry all -out all_seqs.fasta

Prebuilt Databases

Download from NCBI:

# Download and extract (uses update_blastdb.pl)
update_blastdb.pl --decompress nt

# Or download manually from:
# https://ftp.ncbi.nlm.nih.gov/blast/db/

Common databases:

• nt

  - All nucleotide sequences

• nr

  - Non-redundant protein

• refseq_rna

  - RefSeq RNA

• swissprot

  - UniProt SwissProt

Common Errors

BLAST Database error

No hits found

Sequence too short

Out of memory

Local vs Remote BLAST

Decision Tree

Running BLAST locally?
├── Have reference sequences?
│   └── makeblastdb to create database
├── Download NCBI database?
│   └── update_blastdb.pl or manual download
├── Need tabular output?
│   └── -outfmt 6 (or 7 with headers)
├── Filter low-complexity?
│   └── -dust yes (nucl) or -seg yes (prot)
├── Multiple queries?
│   └── Put all in one FASTA, use -num_threads
├── Need XML output?
│   └── -outfmt 5
└── Extract hit sequences?
    └── blastdbcmd -entry

Related Skills

• blast-searches - Remote BLAST via NCBI (no installation needed)
• sequence-io - Read/write FASTA files for queries
• batch-downloads - Download sequences to build local databases