DNA/RNA Sequence Analysis

Usage

1. MCP Server Definition

Use the same BiologyToolsClient class as defined in the protein-properties-calculation skill.

2. DNA/RNA Sequence Analysis Workflow

This workflow analyzes DNA and RNA sequences, calculating molecular weight, GC content, melting temperature, and generating reverse complements.

Workflow Steps:

1. Calculate DNA Molecular Weight - Compute molecular weight for DNA sequences
2. Calculate Oligonucleotide Properties - Compute GC content, Tm, extinction coefficient for RNA
3. Generate Reverse Complement - Create reverse complement sequence

Implementation:

## Initialize client
HEADERS = {"SCP-HUB-API-KEY": "<your-api-key>"}

client = BiologyToolsClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio",
    HEADERS
)

if not await client.connect():
    print("connection failed")
    exit()

print("=== DNA/RNA Sequence Analysis ===\n")

## Step 1: Calculate DNA molecular weight
print("Step 1: DNA Molecular Weight")
dna_sequence = "ATGATGTAACGTAGCTAG"
sequence_para = f"seq1:{dna_sequence}.strand=single,topology=linear"

result = await client.client.call_tool(
    "DNAMolecularWeightCalculator",
    arguments={"sequence_para": sequence_para}
)
result_data = client.parse_result(result)
print(f"DNA Sequence: {dna_sequence}")
print(f"Result:\n{result_data}\n")

## Step 2: Calculate oligonucleotide (RNA) properties
print("Step 2: Oligonucleotide (RNA) Properties")
rna_sequence = "AUGAUGUAACGUAGCUAG"

result = await client.client.call_tool(
    "CalculatorOligonucleotide",
    arguments={"sq": rna_sequence}
)
result_data = client.parse_result(result)
print(f"RNA Sequence: {rna_sequence}")
print(f"Result:\n{result_data}\n")

## Step 3: Generate reverse complement
print("Step 3: Reverse Complement")
test_sequence = "ATCGATCG"

result = await client.client.call_tool(
    "GetReverseComplement",
    arguments={"sequence": test_sequence}
)
result_data = client.parse_result(result)
print(f"Original Sequence: {test_sequence}")
print(f"Reverse Complement:\n{result_data}\n")

## Step 4: Calculate annealing temperature for primers
print("Step 4: PCR Primer Annealing Temperature")
primer_sequence = "GCTAGCTAGCTA"

result = await client.client.call_tool(
    "ComputeAnnealingTemperature",
    arguments={"sequence": primer_sequence}
)
result_data = client.parse_result(result)
print(f"Primer Sequence: {primer_sequence}")
print(f"Result:\n{result_data}\n")

await client.disconnect()

Tool Descriptions

SciToolAgent-Bio Server:

• DNAMolecularWeightCalculator: Calculate DNA molecular weight

  • Args: sequence_para (str) - Formatted sequence with parameters
  • Format: "seqName:SEQUENCE.strand=single/double,topology=linear/circular"
  • Returns: Molecular weight in Daltons

• CalculatorOligonucleotide: Calculate oligonucleotide (RNA) properties

  • Args: sq (str) - RNA sequence
  • Returns: GC content (%), Tm (°C), molecular weight, extinction coefficient

• GetReverseComplement: Generate reverse complement sequence

  • Args: sequence (str) - DNA sequence
  • Returns: Reverse complement sequence

• ComputeAnnealingTemperature: Calculate primer annealing temperature

  • Args: sequence (str) - Primer sequence
  • Returns: Annealing temperature for PCR

Input/Output

Input:

• DNA sequences: Use A, T, G, C nucleotides
• RNA sequences: Use A, U, G, C nucleotides
• Sequence parameters for DNA: strand type (single/double) and topology (linear/circular)

Output:

• DNA Molecular Weight: Mass in Daltons for DNA sequences
• GC Content: Percentage of G and C nucleotides
• Tm (Melting Temperature): Temperature at which 50% of DNA is denatured
• Extinction Coefficient: For nucleic acid quantification (M⁻¹cm⁻¹)
• Reverse Complement: Complementary antiparallel sequence

Use Cases

• Design PCR primers with appropriate annealing temperatures
• Calculate oligonucleotide concentrations spectrophotometrically
• Generate reverse complement for sequencing analysis
• Analyze GC content for primer design
• Plan molecular cloning experiments
• Estimate DNA/RNA molecular weights
• Design and analyze synthetic oligonucleotides

Sequence Format for DNA Molecular Weight

Format: "seqName:SEQUENCE.strand=X,topology=Y"

Parameters:

• seqName: Identifier for the sequence
• SEQUENCE: DNA nucleotide sequence (A, T, G, C)
• strand: Either "single" or "double"
• topology: Either "linear" or "circular"

Example: "plasmid1:ATGCATGC.strand=double,topology=circular"

GC Content and Tm

• High GC content (>60%): Higher melting temperature, more stable
• Low GC content (<40%): Lower melting temperature, less stable
• Tm: Used to determine PCR annealing temperature (typically Tm - 5°C)

Additional DNA/RNA Tools Available

• ORFFind: Find open reading frames
• TranslateDNAtoAminoAcidSequence: Translate DNA to protein
• RepeatDNASequenceSearch: Find repetitive sequences
• CpGIslandPrediction: Predict CpG islands
• PCRPrimerProperties: Analyze primer properties
• RandomDNAGeneration: Generate random DNA sequences
• CircularDNAAlignment: Align circular DNA sequences