Section 49
Chapter 48,618

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

Elnitski, L.; King, D.; Hardison, R.C.

Methods in Molecular Biology 338: 91-103


ISSN/ISBN: 1064-3745
PMID: 16888352
DOI: 10.1385/1-59745-097-9:91
Accession: 048617539

Download citation:  

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/.

PDF emailed within 0-6 h: $19.90