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Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

Carleton L Kingsford*, Kunmi Ayanbule and Steven L Salzberg

Author Affiliations

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA

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Genome Biology 2007, 8:R22  doi:10.1186/gb-2007-8-2-r22

Published: 21 February 2007

Additional files

Additional data file 1:

Complete C++ source code for the TransTermHP system.

Format: ZIP Size: 844KB Download file

Open Data

Additional data file 2:

As described in the text, the entire robust tail-to-tail region is searched; if the region is less than 500 nt, then the 500 nt downstream of the stop codon is searched (stopping if a gene start is encountered). In the case of ties, all terminators with the high score are output.

Format: ZIP Size: 9MB Download file

Open Data

Additional data file 3:

Accession and version numbers for the sequences of each genome used.

Format: TXT Size: 24KB Download file

Open Data

Additional data file 4:

Best terminators found downstream of each of the genes of the 343 organisms studied.

Format: ZIP Size: 29MB Download file

Open Data