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Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA.

Authors
  • Elnitski, Laura
  • King, David
  • Hardison, Ross C
Type
Published Article
Journal
Methods in Molecular Biology
Publication Date
Jan 01, 2006
Volume
338
Pages
91–103
Identifiers
PMID: 16888352
Source
Medline
License
Unknown

Abstract

One major goal of genomics is to identify all the functional sequences in genomes, including sequences that regulate the expression of genes. Sequence conservation is a good, albeit imperfect, guide to these functional elements. We describe how to use publicly available servers (Galaxy, the UCSC Table Browser, and GALA) to find genomic sequences whose alignments (from blastZ and multiZ) show properties associated with cis-regulatory modules, such as high conservation score, high regulatory potential score, and conserved transcription factor binding sites. Links to these servers can be accessed at http://www.bx.psu.edu/ and http://genome.ucsc.edu/.

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