How to compare two genomes at nucleotide level
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7.5 years ago

Hello,

I just started to learn Biopython. Please help me with this.

Compare both genomes NC_019495.1 and NC_019491.1 on a nucleotide level. For that purpose I have to iterate over both genomes with a meaningful window-size. For every window I got to save the window start position. For each window in genome A, how to find exact matches in genome B and save the corresponding position. I should have for every window two coordinates. Plot them in a scatterplot and create a syntenic plot. Can anyone help me with this.

Thanks a lot.

alignment biopython • 2.8k views
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7.5 years ago
lomereiter ▴ 470

Is this merely for the purpose of studying Python? If yes, you can whip up an algorithm in this way, but in all likelihood it will be awfully slow compared to solid tools such as MUMmer.

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Thanks for your reply. I was asked to write a python code for it but not to use any tools.

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Got it. BioPython has very decent documentation. What you're describing is present there as well - read http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec356

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Thank you for your answer and your help. In that document, it is for two records of same genome. But I have to do it on two different genomes. That's where I got stuck. I hope you understood.

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