Locating potential enhancer elements by comparative genomics using the EEL software

Kimmo Palin; Jussi Taipale; Esko Ukkonen

doi:10.1038/nprot.2006.56

Locating potential enhancer elements by comparative genomics using the EEL software

Nat Protoc. 2006;1(1):368-74. doi: 10.1038/nprot.2006.56.

Authors

Kimmo Palin¹, Jussi Taipale, Esko Ukkonen

Affiliation

¹ Department of Computer Science, P.O. Box 68 (Gustaf Hällströmin katu 2b) FIN-00014, University of Helsinki, Finland. Kimmo.Palin@helsinki.fi

PMID: 17406258
DOI: 10.1038/nprot.2006.56

Abstract

This protocol describes the use of Enhancer Element Locator (EEL), a computer program that was designed to locate distal enhancer elements in long mammalian sequences. EEL will predict the location and structure of conserved enhancers after being provided with two orthologous DNA sequences and binding specificity matrices for the transcription factors (TFs) that are expected to contribute to the function of the enhancers to be identified. The freely available EEL software can analyze two 1-Mb sequences with 100 TF motifs in about 15 min on a modern Windows, Linux or Mac computer. The output provides several hypotheses about enhancer location and structure for further evaluation by an expert on enhancer function.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Computational Biology / methods*
Enhancer Elements, Genetic*
Genomics / methods*
Sequence Analysis, DNA
Software*
Transcription Factors / metabolism

Substances

Transcription Factors