TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator. TransTermHP is described in:
Carl Kingsford, Kunmi Ayanbule, and Steven Salzberg. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biology 8:R22 (2007).A predecessor system, TransTerm, that used very different search and scoring algorithms is described in:
Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial Genomes. J Mol Biol 301, (1), 27-33 (2000)
Source code for version 2.09 (updated Feb 28, 2011) can be downloaded here. This version has been tested on Linux, but should compile on most UNIX-like systems using GCC. See the included USAGE.txt file for how to use TransTermHP.
Last Update : April, 2015. The database now contains 2773 genomes.
To download predictions by organism, visit the Download Predictions tab. To search predicted terminators, visit the Search Terminators tab.
For questions or to report bugs, email firstname.lastname@example.org
This project is supported in part by NIH Award R01-GM083873.