lamm-mit/blast

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)