Sequence Analysis

Analyze sequence properties including GC content, restriction sites, and more.

Overview

Kernel provides tools to analyze:

• Sequence composition

• Restriction enzyme sites

• Melting temperature

• Open reading frames

• Sequence patterns

GC Content

View GC Content

GC percentage appears in the status bar when:

• Viewing a construct (total GC%)

• Selecting a region (selection GC%)

GC Content Analysis

Analyze GC distribution:

• Overall percentage

• Regional variation

• GC-rich/AT-rich regions

Why GC Content Matters

• Affects DNA stability

• Influences PCR primer design

• Impacts expression levels

• May indicate horizontal gene transfer

Restriction Site Analysis

Access Cut Sites Tool

1. Open a construct

2. Click Cut sites in the right sidebar

3. View restriction enzyme sites

Features

• List of enzymes that cut the sequence

• Number of cut sites per enzyme

• Position of each cut site

• Visualization on sequence

Filtering Enzymes

Filter by:

• Number of cuts (unique cutters, double cutters, etc.)

• Enzyme type

• Recognition sequence length

• Commercial availability

Common Use Cases

• Find unique cutters for cloning

• Identify sites to avoid

• Plan restriction digests

• Verify correct assembly

Melting Temperature

Selection Tm

Select a region to see estimated melting temperature in the status bar.

Tm Calculation

Kernel calculates Tm using standard methods considering:

• Sequence length

• GC content

• Salt concentration

• Primer concentration

Applications

• Primer design

• PCR optimization

• Hybridization experiments

Open Reading Frame Analysis

Find ORFs

1. View > Show ORFs

2. ORFs highlight in the sequence

3. Click to see ORF details

ORF Information

Each ORF shows:

• Start and stop positions

• Reading frame (1, 2, 3 or -1, -2, -3)

• Length in codons

• Start codon type

Use Cases

• Identify potential coding regions

• Verify gene annotations

• Find alternative reading frames

Sequence Search

Within Construct

1. Click Search in right sidebar

2. Enter search sequence

3. Navigate between matches

Search Options

• Case insensitive matching

• Ambiguous base support (N, R, Y, etc.)

• Reverse complement search

Sequence Statistics

Basic Statistics

View in Info panel:

• Total length (bp)

• GC content (%)

• Molecular weight

• Extinction coefficient

Composition

Nucleotide frequency:

• A count and percentage

• T count and percentage

• G count and percentage

• C count and percentage

Export Analysis

Export Options

• Copy statistics to clipboard

• Download as text report

• Include in construct export

Sequence Tools Integration

Combine with other tools:

Tool	Analysis Use
BLAST	Find similar sequences
Codon Optimization	Analyze before/after
Simulation	Connect analysis to predictions

Next Steps

• Sequence Viewer — Navigate sequences

• Codon Optimization — Optimize for expression

• BLAST Search — Find similar sequences