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IGB searching supports regular expressions and wild cards. This is especially useful when searching for sequence motifs, such as transcription factor binding sites.
Example queries:
Pattern | Represents | Example | Finds |
. | any single nucleotide | ACCT.T | ACCTTT, ACCTAT, ACCTGT, and ACCTCT (4 possibilities) |
.. | any two nucleotides | ACCT..T | ACCTAAT, ACCTATT, ACTAGT, Etc. (4 x 4 possibilities) |
[CG] | a C or a G | ACCT[CG]TC | ACCTCTC and ACCTGTC |
T{1,n} | 1 to n T's | ACGGT{1,3}C | ACGGTC, ACGGTTC, ACGGTTTC |
T* | Zero or more T's | ACGGT*C | ACGGC, ACGGTC, ACGGTTC, ACGGTTTC, ACGGTTTTTTTTTTTTTTTTTTTTTTTTTTTC, Etc. |
.*? | a string of any length containing any nucleotides | TCGGGGTTAA.*?CTGGACTC | Many possibilities. Because this allows for so many possibilities, it only recommended with a limited scope of search and/or with very specific (several specified base pairs) on both ends. |
.* | the longest possible string of any length containing any nucleotides | TCGGGGTTAA.*CTGGACTC | Differs from the search above in that the longest possible result(s) will be found. Bear in mind that the result returned from this search with depend on the scope of the search, ie how much of the genomic sequence has been loaded and is available for searching. |
| R | a A or a G | GCCR | GCCA, GCCG |
| Y | a C or a T | AGCY | AGCY, AGCT |
| S | a G or a C | AGCS | AGCG, AGCC |
| W | a A or a T | AWGC | AAGC, ATGC |
| K | a G or a T | AKGC | AGGC, ATGC |
| M | a A or a C | AMGC | AAGC, ACGC |
| B | a C or a G or a T | ABGC | ACGC, AGGC, ATGC |
| D | a A or a G or a T | ADGC | AAGC, AGGC, ATGC |
| H | a A or a C or a T | AGHC | AGAC, AGCC, AGTC |
| V | a A or a C or a G | AGVC | AGAC, AGCC, AGGC |
| N | any base i.e. a A or a G or a T or a C | AGCN | AGCA, AGCG, AGCT, AGCC |
More information about regular expressions is available from http://docs.oracle.com/javase/7/docs/index.html.