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:
C. Kingsford, K. Ayanbule and S.L. 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. (TransTermHP 1.0 was an internal release.)
For questions or to report bugs, email transterm [AT] umiacs.umd.edu.