# BLAST Search

Find similar sequences across your workspace and public databases.

## What is BLAST?

BLAST (Basic Local Alignment Search Tool) finds sequences similar to your query. Use it to:

* Find related constructs or parts
* Identify homologs
* Check for unintended sequence matches
* Verify construct identity

## Running BLAST

### Access BLAST

1. Press **Cmd/Ctrl + K** to open global search
2. Enter your query sequence or search term
3. Use the BLAST search option to find similar sequences

Or from the construct editor:

1. Select a sequence region
2. Right-click > **BLAST selection**

### Input Query

Enter your query sequence:

* Paste nucleotide sequence
* Select from open construct
* Enter accession number

### Configure Search

**Search Database:**

* Workspace constructs
* Workspace parts
* Public databases

**Search Type:**

* blastn (nucleotide vs. nucleotide)
* blastx (translated nucleotide vs. protein)
* tblastn (protein vs. translated nucleotide)

**Parameters:**

* E-value threshold
* Word size
* Gap penalties

## Understanding Results

### Results Table

| Column   | Description              |
| -------- | ------------------------ |
| Hit      | Matching sequence name   |
| Score    | Alignment score          |
| E-value  | Statistical significance |
| Identity | Percent identical        |
| Coverage | Query coverage           |
| Location | Repository and position  |

### Alignment View

Click a result to see:

* Sequence alignment
* Matching regions
* Gaps and mismatches

### E-value Interpretation

| E-value        | Meaning                    |
| -------------- | -------------------------- |
| < 1e-50        | Very strong match          |
| 1e-50 to 1e-10 | Strong match               |
| 1e-10 to 1e-5  | Moderate match             |
| > 1e-5         | Weak match (may be random) |

## Using Results

### Navigate to Hit

Click a result to open the matching construct or part in a new tab.

## Search Strategies

### Find Similar Parts

1. Enter your part sequence
2. Search workspace parts
3. Find existing similar parts
4. Avoid redundant creation

### Verify Constructs

1. BLAST your construct
2. Check expected hits appear
3. Look for unexpected matches
4. Verify correct assembly

### Find Homologs

1. Enter gene sequence
2. Search public databases
3. Identify orthologs/paralogs
4. Guide phylogenetic analysis

## Best Practices

### Query Selection

* Use representative region
* Avoid repetitive sequences
* Include enough context (>50 bp)

### Result Analysis

* Check E-values for significance
* Verify alignments make sense
* Consider biological context

## Troubleshooting

### No Results

* Check query sequence validity
* Search additional databases

### Too Many Results

* Use longer query sequence

### Slow Search

* Large databases take time
* Use more specific databases

## Next Steps

* [SecureDNA Scanner](/tools/secure-dna.md) — Biosecurity screening
* [Search](/repositories-and-organization/search.md) — Text-based search
* [Sequence Analysis](/sequence-tools/analysis.md) — Other analysis tools


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