Database for codon number

[johnsequence]

Hi, Everyone

I am wondering which database I should download to annotate the codon number of my variant calling derived from DNA sequencing (DNA codon database?), specially on cancer gene like KRAS condon number. If the coordinate of these codon is available, it would be great!

Thanks.

John

[adamdeluca]

look into something like snpEff or Annovar

[johnsequence]

look into something like snpEff or Annovar

Hi adamdeluca,

Thanks for your info. I did run annotation using both snpEff and annovar. One example was shown below. It seemed that coding
inf like ENST00000256078 was there, but the codon number like codon 12 is not shown up. For systemic computation, it would be bettter to get a database containing a piece of info of codon number and I am wondering where I should get it. Thanks. John

DP=125;AF=0.033;NP=30;PV=2.736857973977591E-36;EFF=DOWNSTREAM(MODIFIER||||KRAS|protein_coding|CODING|ENST00000256078|),DOWNSTREAM(MODIFIER||||KRAS|protein_coding|CODING|ENST00000311936|),DOWNSTREAM(MODIFIER||||KRAS|protein_coding|CODING|ENST00000557334|),DOWNSTREAM(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000554266|),DOWNSTREAM(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000555711|),DOWNSTREAM(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000556198|),DOWNSTREAM(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000556351|),DOWNSTREAM(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000556402|),DOWNSTREAM(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000556927|),INTRON(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000553788|),UTR_3_PRIME(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000381356|),UTR_3_PRIME(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000556885|),UTR_3_PRIME(MODIFIER||||LYRM5|protein_coding|CODING|ENST00000557540|)