- FastFind was made for ESTs but could also be applied to any genome. It's pretty straightforward, by bit-packing sequences into a mysql database and searching for combinations. Well, anyways, at least they got their paper accepted.
- _tfloc_ by Matt Weirauch, used in USCS genome browser but not on the net yet (also with alignments)
- Fuzznuc of the well-known EMBOSS package is a little program that can scan sequences against Consensi and report back matches. It knows about mismatches, but can not search for combinations of Consensi.
- tacg seems good TODO
- Alibaba2 Is a special kind of Matrix Scanning Algorithm: It's using Transfac's site table, not the matrices themselves. Some people prefer it to matrix matching, especially those who don't trust Transfac's team to really put similar sites into matrices. [Note: Link is dead. Sept 05] (A paper describing the software is available here: gcb99 alibaba)
- Patmatch (article) from tair can search for flexible spacers, repeats, similar to regulat expressions.
- Patscan can do more, has a grammar-style language for patterns which is quite powerful but probably too complex for promoter-analysis.
- STAN is a suffix tree with a kind of variables, inspired by grammars. The software is similar to Patscan but fast enough for whole genome searches. Yet, you cannot download the source code, which makes it unusable for most people at the moment.