blast

Research

Search NCBI BLAST for sequence homology and find similar sequences in biological databases

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BLAST Search

Run NCBI BLAST (Basic Local Alignment Search Tool) searches to find sequence homology against NCBI databases.

Overview

BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

Usage

Basic protein BLAST search:

python3 {baseDir}/scripts/blast_search.py --query "MTEYKLVVVGAGGVGKSALTIQLIQ" --program blastp

Nucleotide search:

python3 {baseDir}/scripts/blast_search.py --query "ATGCGATCGATCGATCG" --program blastn

Search from FASTA file:

python3 {baseDir}/scripts/blast_search.py --query /path/to/sequence.fasta --database nr --program blastp

Get detailed output:

python3 {baseDir}/scripts/blast_search.py --query "SEQUENCE" --program blastp --format detailed --max-hits 20

Parameters

Parameter	Description	Default
`--query`	Amino acid/nucleotide sequence or path to FASTA file	Required
`--program`	BLAST program: blastn, blastp, blastx, tblastn, tblastx	blastp
`--database`	Database to search: nr, nt, refseq_protein, refseq_rna, swissprot, pdb	nr
`--evalue`	E-value threshold	10.0
`--max-hits`	Maximum number of hits to return	10
`--format`	Output format: summary, detailed, json	summary

BLAST Programs

blastp: Protein query vs protein database
blastn: Nucleotide query vs nucleotide database
blastx: Translated nucleotide query vs protein database
tblastn: Protein query vs translated nucleotide database
tblastx: Translated nucleotide query vs translated nucleotide database

Databases

nr: Non-redundant protein sequences
nt: Non-redundant nucleotide sequences
refseq_protein: NCBI Reference Sequence protein database
refseq_rna: NCBI Reference Sequence RNA database
swissprot: Swiss-Prot protein database (curated)
pdb: Protein Data Bank sequences

Examples

Find similar proteins to human p53:

python3 {baseDir}/scripts/blast_search.py --query "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP" --program blastp --database swissprot

Search for homologs with strict E-value:

python3 {baseDir}/scripts/blast_search.py --query "MTEYKLVVVGAGGVGKSALTIQLIQ" --evalue 0.001 --max-hits 50

Output

The tool returns:

Hit accession and description
E-value and bit score
Percent identity and alignment length
Query and subject coverage
Alignment details (in detailed mode)

Notes

BLAST searches are submitted to NCBI servers and may take 30 seconds to several minutes
For large-scale searches, consider using local BLAST+ installation
NCBI requests that you provide an email for heavy usage (set NCBI_EMAIL environment variable)