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.

Add to Construct

1. Select a hit

2. Click Add to construct

3. Choose destination construct

4. Insert the matching sequence

Export Results

• Download as CSV

• Copy alignment to clipboard

• Save search for reference

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)

Database Selection

• Start with workspace search

• Expand to public if needed

• Use appropriate search type

Result Analysis

• Check E-values for significance

• Verify alignments make sense

• Consider biological context

Troubleshooting

No Results

• Check query sequence validity

• Broaden E-value threshold

• Search additional databases

Too Many Results

• Tighten E-value threshold

• Use longer query sequence

• Filter results by coverage

Slow Search

• Large databases take time

• Consider shorter query

• Use more specific databases

Next Steps

• SecureDNA Scanner — Biosecurity screening

• Search — Text-based search

• Sequence Analysis — Other analysis tools