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BLAST Search Guide

This guide explains how to use the BLAST search functionality in the Electron Genome Viewer application.

Overview

The Genome Viewer includes comprehensive BLAST search capabilities that allow you to:

  • Search sequence similarity against NCBI databases
  • Perform batch searches with multiple sequences
  • Use advanced filtering and algorithm parameters
  • Integrate with local BLAST servers via MCP

Using the UI

  1. Open BLAST Search: Click the "BLAST" button in the top toolbar
  2. Select BLAST Type: Choose from blastn, blastp, blastx, or tblastn
  3. Input Sequence:
  4. Type/paste sequence directly
  5. Upload a FASTA file
  6. Load sequence from current genomic region
  7. Choose Database: Select from available NCBI databases
  8. Set Parameters: Adjust E-value, max targets, etc.
  9. Run Search: Click "Run BLAST" to execute

Using Chat/LLM Interface

You can perform BLAST searches through the chat interface using natural language or tool calls:

Natural Language Examples:

  • "BLAST this sequence against the nucleotide database: ATGCGCTATCG"
  • "Search for protein similarity: MKELLKAGWKELQP"
  • "BLAST the current genomic region"

Tool Call Examples:

{
  "tool_name": "blast_search",
  "parameters": {
    "sequence": "ATGAAAGAATTGAAAGAAGCTGGCTGGAAAGAACTGCAGCCG",
    "blastType": "blastn",
    "database": "nt",
    "evalue": "0.01",
    "maxTargets": 50
  }
}

Advanced BLAST Features

Search multiple sequences simultaneously:

{
  "tool_name": "batch_blast_search",
  "parameters": {
    "sequences": [
      { "id": "gene1", "sequence": "ATGCGCTATCG" },
      { "id": "gene2", "sequence": "ATGAAAGAATT" }
    ],
    "blastType": "blastn",
    "database": "nt",
    "maxTargets": 10
  }
}

Advanced Search with Filtering

Perform BLAST with custom algorithms and result filtering:

{
  "tool_name": "advanced_blast_search",
  "parameters": {
    "sequence": "ATGCGCTATCG",
    "blastType": "blastn",
    "database": "nt",
    "filters": {
      "minIdentity": 95,
      "minCoverage": 80,
      "maxEvalue": 1e-10
    },
    "algorithms": {
      "wordSize": "11",
      "matrix": "BLOSUM62"
    }
  }
}

Search Current Genomic Region

BLAST the sequence from a specific genomic region:

{
  "tool_name": "blast_sequence_from_region",
  "parameters": {
    "chromosome": "NC_000913.3",
    "start": 3423681,
    "end": 3424651,
    "blastType": "blastn",
    "database": "refseq_genomic"
  }
}

Available Databases

Nucleotide Databases

  • nt: Nucleotide collection (all GenBank+EMBL+DDBJ+PDB sequences)
  • refseq_rna: RefSeq RNA sequences
  • refseq_genomic: RefSeq Genome sequences

Protein Databases

  • nr: Non-redundant protein sequences
  • swissprot: UniProtKB/Swiss-Prot
  • pdb: Protein Data Bank proteins

BLAST Types

  • blastn: Nucleotide sequence vs nucleotide database
  • blastp: Protein sequence vs protein database
  • blastx: Translated nucleotide sequence vs protein database
  • tblastn: Protein sequence vs translated nucleotide database

MCP BLAST Server Integration

For advanced features like local databases and batch processing, you can set up a local BLAST server.

Setting Up Local BLAST Server

  1. Install BLAST+:
# On macOS with Homebrew
brew install blast

# On Ubuntu/Debian
sudo apt-get install ncbi-blast+

  1. Set up databases (optional for local databases)

  2. Run example MCP BLAST server:

cd examples
node mcp-blast-server.js
  1. Configure in Genome Viewer:
  2. The BLAST server is pre-configured at ws://localhost:3002
  3. Enable it in the MCP Server Manager if needed

MCP BLAST Server Features

When connected to an MCP BLAST server, you get additional capabilities:

  • Local database searches
  • Batch processing optimization
  • Custom algorithm parameters
  • Database creation and management

Parameters Reference

Basic Parameters

  • sequence: Query sequence (required)
  • blastType: Type of BLAST search (required)
  • database: Target database (required)
  • evalue: E-value threshold (default: 0.01)
  • maxTargets: Maximum number of results (default: 50)

Advanced Parameters

  • wordSize: Word size for initial matching
  • matrix: Scoring matrix (BLOSUM62, PAM30, etc.)
  • gapOpen: Gap opening penalty
  • gapExtend: Gap extension penalty
  • lowComplexity: Filter low complexity regions

Filtering Options

  • minIdentity: Minimum identity percentage
  • minCoverage: Minimum coverage percentage
  • maxEvalue: Maximum E-value threshold
  • excludePatterns: Patterns to exclude from descriptions

Result Interpretation

BLAST results include:

  • Accession: Database identifier
  • Description: Sequence description
  • Score: Alignment score
  • E-value: Expect value (lower = more significant)
  • Identity: Percentage sequence identity
  • Coverage: Query coverage percentage
  • Alignment: Sequence alignment details

Tips and Best Practices

  1. Choose appropriate databases:
  2. Use nt for general nucleotide searches
  3. Use nr for general protein searches

  4. Use RefSeq databases for high-quality sequences

  5. Adjust E-value thresholds:

  6. Stricter (lower) for specific matches

  7. More relaxed (higher) for distant homologs

  8. Use batch searches for multiple queries

  9. Apply filters for high-specificity searches

  10. Check alignment details for verification

Troubleshooting

Common Issues

  1. "BLAST functionality not available":
  2. Check that BlastManager is initialized

  3. Verify internet connection for NCBI searches

  4. "Sequence too short":

  5. Minimum sequence length is 10 characters

  6. Ensure sequence contains valid nucleotides/amino acids

  7. "Connection timeout":

  8. Check internet connection

  9. Try reducing maxTargets parameter

  10. "No results found":

  11. Try relaxing E-value threshold
  12. Check sequence for errors
  13. Try different databases

Getting Help

  • Check browser console for detailed error messages
  • Use the chat interface to ask for help with BLAST searches
  • Refer to NCBI BLAST documentation for parameter details

Examples

DNA Sequence Analysis

{
  "tool_name": "blast_search",
  "parameters": {
    "sequence": "ATGAAAGAATTGAAAGAAGCTGGCTGGAAAGAACTGCAGCCG",
    "blastType": "blastn",
    "database": "nt"
  }
}

{
  "tool_name": "blast_search",
  "parameters": {
    "sequence": "MKELLKAGWKELQPIKEYGIEAVALAYTYQKEQDAIDKELKENITPNVEKKLVWEALKLK",
    "blastType": "blastp",
    "database": "nr"
  }
}

{
  "tool_name": "advanced_blast_search",
  "parameters": {
    "sequence": "ATGAAAGAATTGAAAGAAGCTGGCTGG",
    "blastType": "blastn",
    "database": "nt",
    "filters": {
      "minIdentity": 98,
      "maxEvalue": 1e-20
    }
  }
}