SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences

Fathi Elloumi¹ and Martha Nason²

¹Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Blg50/R5505, Bethesda, MD 20892, USA

²Biostatistics Research Branch, Office of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 6700B Rockledge Dr. MSC 7609, Bethesda, MD 20892-7609, USA

author email corresponding author email

BMC Bioinformatics 2007, 8:354doi:10.1186/1471-2105-8-354


Published:	20 September 2007

Additional files

Additional file 1:

The data sets. This file contains the input sequences and known sites for each TF used in our experiments.

Format: TXT Size: 29KB Download file

Additional file 2:

Searchpattool's results for test1. This file contains the best patterns as predicted by Searchpattool for each of the fourteen TF examined in test1.

Format: XLS Size: 146KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Searchpattool's results for test2. This file contains the best patterns as predicted by Searchpattool for each of the fourteen TF examined in test2.

Format: XLS Size: 3.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

Runtime and number of patterns statistics. This file contains detailed results for the study of runtime and number of patterns found by Searchpattool on random data sets.

Format: XLS Size: 34KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 5:

Searchpattool's software. This archive file contains the application, the source code; a runable example and an explanation of the use of the programs (file readme-searchpattool-doc.pdf)

Format: ZIP Size: 2.9MB Download file