A. Bacterial

Promoter Prediction by Neural Network (Martin Reese, Lawrence Berkeley Laboratory, CA, U.S.A.)

Promoters: (Softberry) - choose from BPROM (bacterial), TSSP (plant) and TSSG & TSSW (human)

PromScan (modified by S. Richards, Queen's University, Canada). Scans small genomes for potential (RpoN) sigma54-RNAP- binding sites. If a *.ptt file is included the results will indicate the position of the promoter relative to the nearest gene. (Reference: D.J. Studholme & R. Dixon. 2003. Domain architectures of sigma54-dependent transcriptional activators. J. Bacteriol. 185:1757-67).

Virtual Footprint - offers two types of analyses (a) Regulon Analysis - analysis of a whole prokaryotic genome with one regulator pattern and (b) Promoter analysis - Analysis of a promoter region with several regulator patterns (Reference: R. Münch et al. 2005. Bioinformatics 2005 21: 4187-4189).

Prokaryotic promoter analysis using SAK (Dept. Computer Science, Royal Holloway, University of London, England) - allows analysis of moderately long sequences for prokaryotic Sigma-70 promoters using Sequence Alignment Kernel method. It was tested on a set of 669 known sigma-70 promoters of Escherichia coli . Error rate 16.5% on promoter-positive sequence data and 18.6% on negative data. (Reference: L. Gordon et al. 2003. Bioinformatics 19:1964-71).

PPP - Prokaryotic Promoter Prediction (Groningen Biomolecular Sciences and Biotechnology Institute, Haren, the Netherlands) - determines from input sequences the putative promoter sequences by using multiple HMM models and presents the results in the following manner:

 SCOPE (Suite for Computational identification Of Promoter Elements), an ensemble of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. (Reference: J.M. Carlson et al. 2007. Nucl. Acids Res. 35: W259-W264)

B. Eukaryotic

Not being a eukaryotic molecular biologist I cannot comment on utility and accuracy of the following promoter- prediction programs. You might want to visit The Eukaryotic Promoter Database and download their organism-specific promoter databases to test the following.  

Neural Network Promoter Prediction (Berkeley Drosophila Genome Project, U.S.A.) (Reference: M.G. Reese 2001. Comput. Chem. 26: 51-6).
Promoter 2.0 Prediction Server (S. Knudsen,Center for Biological Sequence Analysis, Technical University of Denmark) - predicts transcription start sites of vertebrate Pol II promoters in DNA sequences
PROMOSER - Human, Mouse and Rat promoter extraction service (Boston University, U.S.A.) - maps promoter sequences and transcription start sites in mammalian genomes. (Reference: S. Anason et al. 2003. Nucl. Acids. Res. 2003 31: 3554-59).
Promoter and gene expression regulatory motifs search (Softberry, U.S.A.) - offers a variety of promoter- scanning programs  

C. Transcriptional terminators

TransTerm (Michael Nuhn, Nano+Bio-Center) - TransTerm searches for rho-independent terminators in the vicinity of annotated genes. This TIGR program can be accessed online in two ways. If you have the genome in GenBank format to use this program since it will only look for terminators in the vicinity of the annotated genes. Open "Sequence Analysis" and click on "TransTerm." If the genome has not been annotated use this site. Open "Annotation" and choose Glimmer, RBSfinder with TransTerm.
 TransTermHP (A. Villegas, Public Health Agency of Canada) - an online version of TranstermHP, Reference: Kingsford, C. et al. 2007. Genome Biol. 8: R22) an updated version of TransTerm (Reference: Ermolaeva, M.D. et al. 2000. J Mol Biol 301:27-33)

FindTerm (Softberry Inc.) - can also be used for mapping rho-independent terminators. You might consider using the advanced feature options and minimally increase the default energy threshold to -12.0. Please note that the online version of this program will only find one terminator at a time.  If you are dealing with a long sequence, once you have located a terminator, delete it from the DNA sequence and resubmit.

RibEx: Riboswitch Explorer - scans <40kb DNA for potential genes (which are linked to BLASTP) and several hundred regulatory elements, including riboswitches. If you click on the "search for attenuators" it finds terminators and antiterminators. (Reference: C. Abreu-Goodger & E. Merino. 2005. Nucl. Acids Res. 33: W690-W692).