how to create mutant DNA sequence

Hi, all!

I'm trying to generate mutant sequence based on the type as shown on the far right column of example data below.

transcript  position    mutation    type    WT.seq  MUT.seq
trx1    5   A>G substitution    AAAAAA  AAAAGA
trx2    3   C>CTT   insert  CCCCCC  CCCTTCCC
trx3    7   TTTT>T  deletion    AAAAAATTTT  AAAAAAT

I managed to generate 'Substitution' mutants, but I've got no clue how to make INDEL sequences. Can someone help me solve this?

R, Python, bash, or etc. Any language would be find~

Thank you!

mutation in silico mutagenesis

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written 5.7 years ago by mbk0asis

can you share the code you used to get the substitution mutants? Perhaps it can be extended to also get the other types.

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written 5.7 years ago by lieven.sterck

Hi! Thank you for reply!

I used substring in R to replace a string at a specific position.

substring(test$WT.seq, first=5) <- "G"

It replaces a string in the 5th position to "G".

It's not the actual code I used, but the approach is the same.

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written 5.7 years ago by mbk0asis

I'm far from an expert in R but can't you than not expand it for the other cases?

at least for the insertion it should be doable, no? (in stead of changing it to a G, change it to 'CTT' or such) For the deletions it might indeed be more tricky (unless you can specify that it should not a be single position but a sort of substring?)

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written 5.7 years ago by lieven.sterck

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