To whom it may concern,

I try to convert dbSNP data into predicted Proteinvariants in fast format (in this case the human gene fus (ENSG00000089280).

In my example, I retrieved the rs numbers from the ncbi dbSNP and exported the data

(inquire: (FUS[Gene Name]) AND pathogenic[Clinical Significance])

to .bed and/or vcf file.

My aim is to generate (prediced) protein sequences (e.g the refSeq sequence, but with the according mutation) from human indel or single point mutations. I try to get my hand on CustomProDB, but my R skills are limited so far.

Example .bed file:

track name=dbSNP_human description="dbSNP Build 142 ()" date="2015-04-19 10:00" taxId=9606 dbSnpBuild=142 URL="http://www.ncbi.nlm.nih.gov/snp" assembly= assemblyAccession=
chr16    31191407    31191408    rs121909667    0    +
chr16    31191417    31191418    rs121909668    0    +
chr16    31191409    31191410    rs121909669    0    +
chr16    31191418    31191419    rs121909671    0    +
chr16    31190397    31190398    rs186547381    0    +
chr16    31191088    31191089    rs267606831    0    +
chr16    31185060    31185061    rs267606832    0    +
chr16    31191426    31191427    rs267606833    0    +
chr16    31191051    31191052    rs387906627    0    +
chr16    31185030    31185031    rs387906628    0    +
chr16    31189157    31189158    rs387907274    0    +

I would be very thankful if someone could help me to generate protein sequences from DNA .bed files (or similar) in the future.

Please shout if I forget important things to mention, or If my question needs to moved to another forum path.

Many thanks,
Julian