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Question: aaVariation function bug (Methonine instead of Leucine)
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gravatar for georges.bedran
3 days ago by
georges.bedran0 wrote:

Hello,

I'm currently working on a proteogenomics project, and using customProDB to generate a custom protein database, it's a great R package and i find it really helpful.

However, I recently discovered a bug with the aaVariation function were Leucine is predicted as Methionine.

# R example :

> mtab[2,]
  txid        genename          txname         proname chr strand      pos refbase varbase pincoding       rsid COSMIC_id refcode varcode
  2  649 ENSG00000138593 ENST00000559471 ENSP00000453854  15      - 49325289       A       C       537 rs11638215      <NA>     CTT     CTG
   vartype aaref aapos aavar
  2 non-synonymous     L   179     M

Since the CTG codon gives leucine and not methionine after translation, i made a correction on the output while waiting for a permanent fix. 

thank you.

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