Entering edit mode
6.5 years ago
Nawaj Shaikh
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0
I am studying SNPs of TLR9 gene. Reference sequence of the same gene is available as an reverse orientation, hence i analyse accordingly. Now i have to submit the identified SNPs to dbSNP data base but validation for the same required forward orientation. Can anybody suggest me simple method to find forward orientation of same gene. Thanks in advance.
It's unclear which data you have and which data you aim to obtain, please elaborate using examples.
Thanks for your interest in answer. I have used UCSC data base (Genomic chr3 (reverse strand):52221080-52226163) as well i also checked with NCBI database: Assembly:GRCh38.p7 (GCF_000001405.33), Chr:3, Location: NC_000003.12 (52221080..52226163, complement) but both are reverse orientation. Now i need (if possible) both databases forward orientation to mention position during submission of my identified SNPs.
Hello Nawaj Shaikh,
I'm still not completly sure how your input data looks like. Have you done sanger sequencing and look by hand how your variant should be described on genomic level? Have you just a few variants or a lot? Have they already a dbSNP number or are they all new?
Genomic chr3 (reverse strand):52221080-52226163isn't a complete example of a variant, as you don't say what changes on that position.fin swimmer
Dear Fin, I have been used Genomic chr3 (reverse strand):52221080-52226163 as reference sequence to assess what are SNPs present in my target population. I did snager sequencing after that i have used that data for assess the SNPs through SeqScape software with using above mentioned reference sequence from UCSC as well NCBI data base. Then i found four SNPs, out of two SNPs have already dbSNP number two are new. Hence to submit identified SNPs (all) to dbSNP data base i need to mention positive orientation position of chromosome/gene. Kindly help
If you already described your variant correct on transcript level, you may use mutalyzer's position converter to get the genomic nomenclatur which take the direction of your transcript into account.
fin swimmer
In general, SNPs are reported on forward strand (wrt reference genome) only, except when you are reporting on transcripts. VCF also follows the same and most of the tools report SNPs on forward strand only. If you have identified a SNP on a gene in reverse direction (using any other techniques such as directional cloning), you can complement the gene sequence with corresponding variants and submit to dbSNP. However, if you have used any tool in arriving at SNPs, then cross check output. Btw, how did you arrive at SNPs?