TransTermHP
Transcription Terminator Predictions


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)

Features

Some features of TransTermHP include:
  • Fast due to new dynamic programming algorithm (a typical genome takes < 1 min)
  • New, accurate scoring scheme
  • Informative output
  • Reads gene annotations from either a simple list or .ptt files
  • Handling of overlapping genes & terminators
  • General handling of gaps in terminator hairpins
  • Fully in C++

Download TransTermHP

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.)

Current Predictions

To download predictions by organism, visit the Download Predictions tab. To search predicted terminators, visit the Search Terminators tab.

Contact Us

For questions or to report bugs, email transterm [AT] umiacs.umd.edu.

Acknowledgements

This project is supported in part by NSF Award DBI-0234704 and by NIH Award R01-LM007938.

   
Last updated: Sep. 11, 2006