Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation.

TitleFastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation.
Publication TypeJournal Article
Year of Publication2007
AuthorsElemento O, Tavazoie S
JournalMethods Mol Biol
Volume395
Pagination349-66
Date Published2007
ISSN1064-3745
KeywordsBinding Sites, DNA, Genome, Regulatory Sequences, Nucleic Acid, RNA, Messenger, Sequence Alignment, Transcription Factors
Abstract

Here, we describe the usage of Fastcompare, a simple and efficient comparative approach for finding short noncoding DNA (e.g., transcription factor binding sites) and mRNA (e.g., microRNA target sites) sequences that are globally conserved between two genomes. Fastcompare is based on the network-level conservation principle, according to which the connectivity of transcriptional regulatory networks should be largely conserved between two closely related genomes. We describe here the procedure for applying Fastcompare to large genomes (with an emphasis on metazoan genomes), including scoring of exhaustive motif lists, determination of conservation threshold using sequence randomizations, and discovery of interactions between regulatory elements.

Alternate JournalMethods Mol. Biol.
PubMed ID17993685
Grant ListR56 HG003219 / HG / NHGRI NIH HHS / United States