# Restriction Enzyme Analysis AI Agent Connect

> Analyze DNA digestion patterns, fragment sizes, and enzyme characteristics.

## Overview
- **Category:** science
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_D0skpeu0xtEDdKr6RFQ9fUr16OUucz9XBlZ0PEsu/ai-agent-connect
- **Tags:** dna, enzymes, molecular-biology, genetics, bioinformatics

## Description

This MCP server provides specialized tools for molecular biology research. It allows AI agents to perform precise DNA digestion analysis, including calculating fragment sizes and band patterns using `analyze_digestion_pattern`. Researchers can identify equivalent enzymes via `find_isoschizomers`, predict non-specific cutting with `simulate_star_activity`, and retrieve detailed cutting profiles using `get_enzyme_profile`.

## Tools

### analyze_digestion_pattern
Calculates the primary outcome of a DNA sequence being cut by specific enzymes

### find_isoschizomers
Identifies alternative enzymes that recognize the same sequence

### get_enzyme_profile
Retrieves the specific cutting characteristics of a single enzyme

### simulate_star_activity
Predicts how fragment patterns change when an enzyme exhibits non-specific cutting

## Prompt Examples

**Prompt:** 
```
Analyze the digestion pattern for the sequence ATGCATGCATGC using enzyme EcoRI.
```

**Response:** 
```
The digestion of the sequence results in 3 fragments with sizes of 4, 8, and 4 nucleotides.
```

**Prompt:** 
```
What are the isoschizomers for the enzyme HindIII?
```

**Response:** 
```
The isoschizomers for HindIII include MboI.
```

**Prompt:** 
```
Get the profile for the enzyme BamHI.
```

**Response:** 
```
BamHI recognizes the sequence G/GATCC and produces cohesive (sticky) ends.
```

## Frequently Asked Questions

**How do I calculate fragment sizes?**
You can use the `analyze_digestion_pattern` tool by providing the DNA sequence and the list of enzyme IDs.

**Can I simulate non-specific cutting?**
Yes, the `simulate_star_activity` tool allows you to predict how fragment patterns change when an enzyme exhibits star activity.

**How do I find enzymes with the same recognition site?**
Use the `find_isoschizomers` tool with the specific enzyme ID to find its isoschizomers.