Probe and Primer Search Tool
The Probe and Primer Search Tool allows you to easily search the known coding sequence of any allele, for a particular nucleotide motif. The tool can be used to provide either an online output or a tab separated text file suitable for loading into Excel for use as a hit table or similar.
To use the Probe and Primer Search Tool:
- Simply select the locus and database release required
- Enter the nucleotide sequence or your probe or primer in the box provided. You can enter multiple sequences as long as each sequence is on a separate line.
- To further aid searches approved IUB codes are also permitted within the search string. However due to the number of permutations generated by entering Ns in a sequence, you will be limited to 5 Ns per sequence.
- The search tool only searches the known CDS sequences for each allele, if a probe or primer contains intronic, UTR or pseudoexon sequence, the tool will fail to match this.
- The tool will also not span insertion or deletions with the search string.
- All libraries prior to release 3.0.0 use the pre-2010 nomenclarture designations.
The following IUB Codes can be used in the query sequence. However it should be noted the more ambiguous codes used the slower the search will run.
|IUB Code||Nucleic Acid||IUB Code||Nucleic Acid|
|A||A||Y||C or T|
|C||C||K||G or T|
|G||G||V||A or C or G|
|T||T||H||A or C or T|
|M||A or C||D||A or G or T|
|R||A or G||B||C or G or T|
|W||A or T||N||A or C or G or T|
|S||C or G|