PROMOTERS & TERMINATORS
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)
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).
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)
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 or PlantProm: Plant 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
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 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).
Updated: october 28, 2012