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

ABSTRACT:

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

SUBMITTER: Huang Y 

PROVIDER: S-EPMC520813 | biostudies-literature | 2004 Sep

REPOSITORIES: biostudies-literature