Question: witch software is used to finde a mutation in the DNA sequencsing data. And what the criterai of the computer I need?
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gravatar for roonymoonlight
2.7 years ago by
roonymoonlight40 wrote:

Hi, I have just completed my master degree in Bioinformatics. I still have no experience in DNA sequencing work in wet lab. I got a job to do with capillary sequencing in a hospital. In the analysis of the data. I must find a mutation in the patients samples. Any suggested software? what is the criteria I need in my computer to achieve that ?

sanger sequencing • 855 views
ADD COMMENTlink modified 2.7 years ago by Michael Dondrup46k • written 2.7 years ago by roonymoonlight40
1

You tag "next-gen" but write capillary sequencing (which I assume is Sanger sequencing). So, what is it?
You also didn't specify how many samples you would be working on. Try to be as informative as possible when asking questions.

I'm a bit worried about the content/curriculum of the master's degree you got given this question, but that's definitely beside the point.

ADD REPLYlink written 2.7 years ago by WouterDeCoster41k
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gravatar for Michael Dondrup
2.7 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

You don't need any specific computer for that. If you do sanger seq on a specific gene, you will know the reference gene and most likely have only one or few sequences per patient. Extract the sequence from the chromatogram, see How we can analyze sanger sequence chromatogram? How To Call Snp From .Ab1 Files Of Sanger Sequencing? If you have the sequence already: use exact local alignment e.g. SSearch for an exact alignment of the sanger seq to the reference region in question, you will see the differences immediately in the alignment.

This pipeline can be run on any desktop computer built after year 2000 I guess.

See also https://seqcore.brcf.med.umich.edu/sites/default/files/html/interpret.html http://open-abi-files.en.informer.com/Chromatogram-Viewer/

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Michael Dondrup46k
1

Also useful software: novoSNP (disclaimer: developed in my department)

ADD REPLYlink written 2.7 years ago by WouterDeCoster41k
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