# Sequence Alignment Scoring AI Agent Connect

> Quantify biological similarity for DNA and Protein sequence alignments.

## Overview
- **Category:** science
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_MOpJlaXShDZEs3KPjqoIXX2f0cMXJ4aCcqTmLM3Y/ai-agent-connect
- **Tags:** dna, protein, alignment, scoring, bioinformatics

## Description

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.

## Tools

### 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

## Prompt Examples

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

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

**Prompt:** 
```
Is the sequence 'MKTLL' a valid Protein sequence?
```

**Response:** 
```
Yes, 'MKTLL' is a valid Protein sequence.
```

**Prompt:** 
```
What is the score for aligning residue A with residue G in a specific matrix?
```

**Response:** 
```
The score for aligning residue A with residue G is -1.
```

## Frequently Asked Questions

**What kind of sequences can I analyze?**
You can analyze both DNA and Protein sequences using the `validate_sequence_composition` tool to ensure they are valid.

**How do I choose the right scoring matrix?**
Use the `compare_matrix_capabilities` tool to find recommended matrices based on whether you are working with DNA or Protein.

**Can I get a full statistical summary of an alignment?**
Yes, the `calculate_alignment_metrics` tool provides the alignment score, identity percentage, and similarity percentage.