A. Bacterial

red_bullet.gif (914 bytes) PromoterHunter - is part of phiSITE database which is a collection of phage gene regulatory elements, genes, genomes and other related information, plus tools. (Reference: Klucar, L. et al. 2010. Nucleic Acids Res. 38(Database Issue): D366-D370).

red_bullet.gif (914 bytes) Promoter Prediction by Neural Network   (Martin Reese, Lawrence Berkeley Laboratory, CA, U.S.A.) - applicable to eukaryotes and prokarotes (Reference: Reese MG, 2001. Comput Chem 26: 51-56). Dated and prokaryote results must be viewed skeptically.

red_bullet.gif (914 bytes) Promoters: (Softberry) - choose from BPROM (bacterial), TSSP (plant) and TSSG & TSSW (human)

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).

red_bullet.gif (914 bytes) PePPER (University of Groningen, The Netherlands) is a webserver for prediction of prokaryote promoter elements and regulons (Reference: de Yong, A. et al. 2012. BMC Genomics 13:299).  It is also available here.  Also see Prokaryotic promoters.

red_bullet.gif (914 bytes) 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)

 DOOR2 - Database of prOkaryotic OpeRons -  offers high-performance web service for online operon prediction on user-provided genomic sequences; and, an intuitive genome browser to support visualization of user-selected data. Plus a huge database of transcriptional units. (Reference: X. Mao et al. 2014. Nucleic Acids Res. 42(Database issue): D654-9).

red_bullet.gif (914 bytes) PATLOC (Pattern Locator) (Institute of Bioinformatics, University of Georgia, U.S.A.) - is a new tool for finding sequence patterns in long DNA sequences. For this web-based service, a restricted version of Pattern Locator is used, which estimates the time needed for completion of the search and stops if the estimated CPU time exceeds a certain limit (currently 90 seconds). The CPU time limit was introduced in order to protect the web server from overloading due to requests involving too complex sequence patterns.  If you want to search for Sigma-70 (RpoD)-like promoters the pattern syntax for your search is:  <>{TTGACA(N)[15:18]TATAAT}[4].  N.B. the [4] allows for 4 mismatches - I recommend a maximum of two.  If you only want one strand screened omit the <> at the start. You can restrict the search to intergenic regions (but this will eliminate also matches that partially overlap with genes or use the .patvic.txt output file to find where they are (Jan Mrázek, personal communication).

B. Eukaryotic

Not being a eukaryotic molecular biologist I cannot comment on utility and accuracy of the following promoter- prediction programs.

red_bullet.gif (914 bytes) EPDnew (Eukaryotic Promoter Database) - is a new collection of experimentally validated promoters in human, mouse, D. melanogaster and zebrafish genomes.  Evidence comes from TSS-mapping from high-throughput expreriments such as CAGE and Oligocapping. ChIP-seq experiments on H2AZ, H3K4me3, Pol-II and DNA methylation are also taken into account during the analysis.  Include promoter analysis tools. (Reference: Dreos, R. et al. 2015.  Nucl. Acids Res. 43 (D1):D92-D96).

red_bullet.gif (914 bytes)  Neural Network Promoter Prediction (Berkeley Drosophila Genome Project, U.S.A.) - dated  (Reference: M.G. Reese 2001. Comput. Chem. 26: 51-6).  
red_bullet.gif (914 bytes) 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
red_bullet.gif (914 bytes) 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).
red_bullet.gif (914 bytes) Promoter and gene expression regulatory motifs search (Softberry, U.S.A.) - offers a variety of promoter-scanning programs  

red_bullet.gif (914 bytes) GPMiner - identifies promoter regions and annotates regulatory features in user-input sequences.    The proposed promoter identification method, whose predictive sensitivity and specificity are both ~80%, incorporates the support vector machine (SVM) with nucleotide composition, over-represented hexamer nucleotides and DNA stability.     Additionally, the input sequence also can be analyzed for homogeneity of experimental mammalian promoter sequences.     After identifying the promoter regions, the regulatory features such as transcription factor binding sites, CpG islands, tandem repeats, the TATA box, the CCAAT box, the GC box, over-represented oligonucleotides, DNA stability and GC-content are graphically visualized to facilitate the observation of gene promoters.

C. Transcriptional terminators

 TransTermHP (A. Villegas, Public Health Ontario, 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 Biol301:27-33)

 WebGeSTer - Genome Scanner for Terminators - my favourite terminator search program is finally web enabled.  Please note that if you want to analyze data from a *.gbk file you need to use  their conversion program "GenBank2GeSTer" first. A complete description of each terminator including a diagram is produced by this program.  This site linked to an extensive database of transcriptional terminators in bacterial genome (WebGeSTer DB) (Reference: Mitra A. et al. 2011.  Nucl. Acids Res. 39(Database issue):D129-35).

 ARNold -  finds rho-independent terminators in nucleic acid sequences using two complementary programs, Erpin and RNAmotif. The program colors the terminator stem and loop (References: Gautheret D, Lambert A. 2001.  J Mol Biol. 313:1003–11 & Macke T. et al. 2001. Nucleic Acids Res. 29:4724–4735 ).

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).