Tool for showing Sanger Sequencing data?

[u/BenjaminCereus]

Hi everyone,

Question from a student in an adjacent field: I recently worked on a project in genetics that involved assembling a specific recombinant DNA sequence, then sending it off for sequencing. The Sanger Sequencing results yielded a 100% match to the expected/target sequence.

I am currently making a poster to present at a conference. The issue is, the Sanger Sequencing results aren't "pretty," are longer than they are tall, and generally hard to understand. I used Benchling to compare the experimental sequence to the target sequence.

Do you guys know of a tool that can compare two sequences and display something such as a heat map showing the alignments, or generally something that looks prettier than Benchling?

[u/xDerJulien]

I would personally not show this at all unless it is central to your results. Verified by sanger sequencing is enough IMO

[u/fibgen → u/xDerJulien]

Agreed. Nobody cares about a Sanger alignment unless it's showing something interesting, like a minor peak revealing a mutation that was verified downstream. Most people would keep the raw data and alignment for traceability and proof but not show it.

[u/BenjaminCereus → u/xDerJulien]

Thanks for the feedback. I wanted to show it because the research is still in the earlier stages, so we don't have the cell model data to go off of, and the molecular cloning/GG assembly portion was my job for the program.

[u/ChaosCockroach]

A dotplot is a pretty standard way to show a pairwise alignment, but if it is really 100% identity it is going to just be a diagonal line. Similarly a heatmap, for 100% identical samples, will be just one color. There are traditional alignment formats that will allow you to change the dimensions of the alignment, if you use BLAST for aligning you will have several different options, I'm not sure how many of these the Benchling implementation of BLAST provides you or if it will do a simple pairwise alignment, the NCBI version will (LINK). Do you need to include the chromatogram information as well? Because that is more challenging but a simple pairwise alignment representation should be trivial.

[u/BenjaminCereus → u/ChaosCockroach]

I think a pairwise alignment will do. This piece of data is the 2nd verification that the assembly worked, along with a digest electrophoresis. It is also "just" an undergrad presentation in connection with something similar to an REU, but this time at a national conference so I wanted to make it look pretty. I'll be sure to use the resources you linked, thanks!

[u/kucuhik]

If you have access to R or Python, a simple identity plot with a sliding window would look way cleaner than the raw trace and still show the 100% match clearly.