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Question: aaVariation function bug (Methonine instead of Leucine)
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gravatar for georges.bedran
5 months 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.

ADD COMMENTlink modified 6 weeks ago by xiaojing.wang50 • written 5 months ago by georges.bedran0
0
gravatar for xiaojing.wang
6 weeks ago by
United States
xiaojing.wang50 wrote:
The function has been updated. Thank you. For you reference, in function translate(), codons 'TTG' and 'CTG' translated into 'M' if they located as the 1st codon in the sequence. Xiaojing On Mon, Apr 16, 2018 at 6:52 AM, georges.bedran [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User georges.bedran <https: support.bioconductor.org="" u="" 11010=""/> wrote Question: > aaVariation function bug (Methonine instead of Leucine) > <https: support.bioconductor.org="" p="" 107941=""/>: > > 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. > > ------------------------------ > > Post tags: customprodb, translation > > You may reply via email or visit https://support.bioconductor. > org/p/107941/ >
ADD COMMENTlink written 6 weeks ago by xiaojing.wang50
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