User GuidesSnapGene Assembly and AlignmentAlign Reads to a Reference Sequence

Align Reads to a Reference Sequence

How do I align Sanger traces to a plasmid sequence to confirm cloning or mutagenesis is error free?

Create or Open a Reference Sequence

Use the SnapGene cloning tools to create your predicted sequence. Open the "reference" file in SnapGene.

In this example we validate a plasmid created by In-Fusion cloning.  The predicted plasmid, YIpLac211-TPM1-msGFP, has been generated in SnapGene using the SnapGene In-fusion cloning  tool.

Import and Align Sanger Traces to the Reference

In Sequence view or Map view click the "Show Alignment" button on the Side toolbar.

Use the "Aligned Sequences" menu to import sequencing reads or simply drag and drop the trace files into the "Align with" field.

During import, sequence trace ends will be hidden based on quality using settings defined in Preferences → Traces and Alignments and, if possible, aligned with the reference. In Map view, aligned traces will be depicted as arrows above the reference map.

In this example, 4 primers have been used to sequence across the msGFP insert and the vector/insert fusion boundaries.

Validate the Aligned Sequences

Switch to Sequence view to view and edit the assembly. The top panel #1 shows the reference and features. The bottom panel #2 shows the reference (Original Sequence) and any aligned trace sequences within the field of view.

Click the triangle in the bottom panel to jump to the first discrepancy in the alignment.

View the Sequence and Trace/Chromatogram

Click on the Triangle to expand the trace view.

The expanded trace view provides controls to change display of the peaks, and provides information on trace length and orientation, and a summary of differences compared to the reference.

Edit the Traces or Reference

Correct Miscall Errors in Traces

Insert Bases into 10E_A1_27_M13R

Select the sequence to be corrected and type to add sequence, or hit delete to remove sequence. In the above example, the sequencer has miscalled a compressed AA double peak as a single A, so we have selected the gap and typed "a". Click OK to accepted the insertion of an "a".

Adjust Hiding of Chromatogram Ends

If nucleotide calls near trace ends are unreliable, then drag the slider to manually hide further nucleotides from the end of the trace.

You can also adjust all ends by clicking  Align Sequences → Hide Ends of Aligned Sequence Traces  and choosing a higher or lower stringency. Choose "No Hidden Bases" to reinstate all hidden bases.

Save the File if the Clone is 100% Identical to the Reference

Once all traces are corrected then if all nucleotide positions are in agreement with the reference then do the following.

1. Closed the "Align with" panel.

2. Show the Description panel and check the option "Confirmed experimentally". A green check mark will then appear next to the sequence length indicator showing that the sequence has been confirmed by sequencing.

3. Save the Sequence.

Save the File if the Clone Differs from the Reference

In some cases the clonal sequence may differ from the reference, for example, if mutagenesis of the amplified insert had been performed prior to fusion/ligation, or if an unwanted misincorporation error occurred during PCR.

If  sequencing confirms the sequenced region differs from the reference then you can create a new sequence that combines the reference with the sequenced region.

In this example, Sanger sequencing has confirmed a single point mutation at codon 2 of msGFP, resulting in an amino acid change in the gene product (T → G = amino acid change Asp → Glu).

Select one or more reads that validate any differences with the reference by shift-clicking on the arrows. Arrows will appear blue for selected reads.

Click Aligned Sequences → Replace Original with Aligned → Make New File....

Confirm the sequences that will replace corresponding regions in the reference, then click OK. The sequence will open as a new (unsaved) document.

Examination of the file in sequence view will show that clonal differences in the sequence trace now incorporated into the new sequence. Click File → Save, or File → Save to Collection and choose to save the new sequence to an appropriate location.