PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability

Background: Regulatory regions that function in DNA replication and gene transcription contain specific sequences that bind proteins as well as less-specific sequences in which the double helix is often easy to unwind. Progress towards predicting and characterizing regulatory regions could be accelerated by computer programs that perform a combined analysis of specific sequences and DNA unwinding properties. Results: Here we present PATTERNFINDER, a web server that searches DNA sequences for matches to specific or flexible patterns, and analyzes DNA helical stability. A batch mode of the program generates a tabular map of matches to multiple, different patterns. Regions flanking pattern matches can be targeted for helical stability analysis to identify sequences with a minimum free energy for DNA unwinding. As an example application, we analyzed a regulatory region of the human c-myc proto-oncogene consisting of a single-strand-specific protein binding site within a DNA region that un...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Yanlin Huang, David Kowalski
• Keywords: BMCBI 2004, Helical Stability, Regulatory Regions, Sequences