Tools To Output All Refseq Mrna Sequences With Snp Minor Allele?

Question

[Krisr]

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?

[Neilfws]

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?

[Larry_Parnell]

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).

[Krisr]

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?

Answer 1

[Prateek]

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.