I’m using the Sequenom iPLEX system for genotyping, and need 200bp of 5 and 3 flanking sequence for rs41296860. How do I find this much flanking sequence?
Currently, dbSNP does not have data for long flanks as you request, so you will have to use the following steps to find the rs41296860 flanking sequence you need:1.Go to the Integrated Maps section of the refSNP cluster report for rs41296860.2.Click on NT_021877.18. This will take you to an Entrez Nucleotide report showing rs41296860 and its flanking sequence on the genomic contig3.Since the variation’s position spans the contig (NT_021877.18) between 467055 and 467056, all you have to do is subtract or add the number of bases you want from the variation positions, and type the difference/sum in the range: “from” and “to” boxes (e.g. 467055 – 100 =466955 and 467056 + 100 = 467156 for a flank of 100bp on either side of the variation).4.Click the “Refresh” button to see the fasta sequence in the desired length.
Related Questions
- What was the sequence of events in the Water Bureau’s response to the discovery of potential contamination in the water system?
- How does the system prevent trapped air between UBM/BLM and bump during the wafer bump transfer sequence?
- I’m building a new home. What’s the most efficient heating and cooling system I can get?
