Promoter analysis: gene regulatory motif identification with A-GLAM.
Reliable detection of cis-regulatory elements in promoter regions is a difficult and unsolved problem in computational biology. The intricacy of transcriptional regulation in higher eukaryotes, primarily in metazoans, could be a major driving force of organismal complexity. Eukaryotic genome annotations have improved greatly due to large-scale characterization of full-length cDNAs, transcriptional start sites (TSSs), and comparative genomics. Regulatory elements are identified in promoter regions using a variety of enumerative or alignment-based methods. Here we present a survey of recent computational methods for eukaryotic promoter analysis and describe the use of an alignment-based method implemented in the A-GLAM program.
Mariño-Ramírez
Leonardo
L
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA.
Tharakaraman
Kannan
K
Spouge
John L
JL
Landsman
David
D
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA