MCP For Claude Marketplace
Sequence Alignment Scoring

Sequence Alignment Scoring MCP Connector for Claude

A+

Quantify biological similarity for DNA and Protein sequence alignments.

4 tools Official Updated Oct 1, 2026 Official Vinkius Partner
More Details Connect to Claude

This MCP server provides high-precision tools for biological sequence analysis. It allows AI agents to calculate alignment scores, identity percentages, and similarity percentages for DNA and Protein sequences. Using tools like calculate_alignment_metrics, agents can evaluate the quality of an alignment using specific substitution matrices and gap penalties. It also includes validate_sequence_composition to ensure sequence integrity and compare_matrix_capabilities to select the optimal scoring matrix for a given biological context.

dnaproteinalignmentscoringbioinformatics

4 tools expose this connector's capabilities to your AI agent.

calculate_alignment_metrics

Provides a comprehensive statistical summary of a single sequence alignment

compare_matrix_capabilities

Answers which scoring matrix is most appropriate for a specific biological context

get_matrix_score

Retrieves the specific score for a single pair of aligned residues

validate_sequence_composition

Ensures that the provided sequences only contain valid characters for the biological type being analyzed

See how to talk to your AI agent using Sequence Alignment Scoring.

Calculate the metrics for these two DNA sequences: ATGC- and ATGC.

The alignment score is -1.0, with an identity percentage of 80% and a similarity percentage of 80%.

Is the sequence 'MKTLL' a valid Protein sequence?

Yes, 'MKTLL' is a valid Protein sequence.

What is the score for aligning residue A with residue G in a specific matrix?

The score for aligning residue A with residue G is -1.

You can analyze both DNA and Protein sequences using the `validate_sequence_composition` tool to ensure they are valid.

Related Connectors

Foxentry

Foxentry MCP

12 tools Official

Validate and autocomplete addresses, emails, and phone numbers in forms to eliminate bad data before it enters your systems.

A+ View details →
NEW
protein-per-serving

protein-per-serving MCP

4 tools Official

Calculates protein content per individual serving.

A+ View details →
LLM Token Counter

LLM Token Counter MCP

2 tools Official

Calculate exact and estimated token counts for GPT-4, GPT-4o, Claude, and Llama models.

A+ View details →
NEW
Squad Roster Validator

Squad Roster Validator MCP

4 tools Official

Validates football competition rosters for compliance with age, size, and homegrown rules.

A+ View details →