Question: Tools To Output All Refseq Mrna Sequences With Snp Minor Allele?
4
gravatar for Krisr
8.4 years ago by
Krisr460
United States
Krisr460 wrote:

Hi,

Does anyone have a suggestion on how I may output a list of human mRNA sequences (Refseq NMs) containing the minor (or alternative) allele?

refseq snp • 1.6k views
ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 8.4 years ago by Krisr460

With this type of question, it helps to know from which data you are starting. Do you have some downloaded file with SNP and NM_ accessions that you could point to on the web?

ADD REPLYlink written 8.4 years ago by Neilfws48k

This is a good question because many RefSeq entries for human contain a minor allele. However, we need to know for which population the allele is minor and if 50% allele frequency is your strict cutoff for major vs minor (due to standard deviation for small sample size).

ADD REPLYlink written 8.4 years ago by Larry_Parnell16k

I would like to output every refseq mRNA (all 37,000+) sequences containing the alternative alleles from dbSNP build 132. I don't have a file for the mRNAs, but was hoping I could output this from a known database that might allow for this manipulation?

ADD REPLYlink written 8.4 years ago by Krisr460
1
gravatar for Prateek
8.4 years ago by
Prateek1.0k
Boston, MA
Prateek1.0k wrote:
  1. Create a file containing | NM12345, rsid contained, position | (one seq may contain more than 1 SNP so multiple rows per NM.

  2. get the latest allele frequencies for your chosen population from the hapmap data rep. http://hapmap.ncbi.nlm.nih.gov/downloads/frequencies/?N=D You may choose to compute a weighted average frequencies of all populations - or just start with CEU (caucasian). These files contains RSIDs.

  3. map frequencies of RSIDs from (2) to (1) and find out which NMs contain minor alleles.

ADD COMMENTlink written 8.4 years ago by Prateek1.0k
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