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.

Probe Searches of Nucleotide Coding Sequences
Release
Locus
Output:
Probes: To enter your probes simply type the sequence of each probe on a new line.

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    

Further Information

For more information about the database, queries (including website) or to subscribe to the IPD mailing lists please contact IPD Support.

Please see our licence for our terms of use.