Hello, I have a question related to analyzing Sanger sequenced data. The reference gene is >7 kb long and it has 4 CDS (1900 bp). The gene has 8 allelic forms (1900 bp). My goal is to re-sequence the 4 exons from my material and compare the allelic diversity (if there is any) with the reference alleles. I have Sanger sequenced all my materials and obtained 4 exons for each genotype. My question is how can I start analyzing this data and compare it against the reference alleles? Which software should I use and what should be my approach? Can someone please give me a headstart? Thank you very much.
Regards Anik
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anikcropscience •
We developed open-source web applications to align Sanger chromatogram traces and call variants with respect to a reference genome. You can also do a reference-guided assembly:
Alignment: https://www.gear-genomics.com/sage/
Variant Calling: https://www.gear-genomics.com/indigo/
Reference-guided assembly: https://www.gear-genomics.com/pearl/
Oh, that is cool. But it does not have the desired reference sequence. I can download and upload the ref. seq. though. thank you.
It is a commonly used model plant (wheat), but the gene of interest is not useful for daily research. So, I would use the fast file.
Thank you. No, I am not a command line expert.
Then MEGA would be a good place to start. They have tutorials/online help. Take a look at that first.
Yes. Thank you very much for your help.
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