TY - JOUR
T1 - Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA.
AU - Elnitski, Laura
AU - King, David
AU - Hardison, Ross C.
N1 - Copyright:
This record is sourced from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
PY - 2006
Y1 - 2006
N2 - 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/.
AB - 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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M3 - Article
C2 - 16888352
AN - SCOPUS:33749057091
SN - 1064-3745
VL - 338
SP - 91
EP - 103
JO - Methods in molecular biology (Clifton, N.J.)
JF - Methods in molecular biology (Clifton, N.J.)
ER -