title: A tiered approach to comparative genomics.
abstract: Comparative genomics has emerged as a valuable tool for locating genes, transcription factor motifs and other putative control regions. There are, however, issues that keep comparative genomics from being a straightforward process. These caveats fall into three categories: database, computational and biological. In this review paper, these caveats will be discussed and illustrated using related case studies. The National Center for Biotechnology Information and University of California Santa Cruz genome databases were used, and VISTA, LAGAN and zPicture were used as comparison tools. Based on these caveats, a tiered approach to carrying out comparative genomic studies is presented.
authors.affiliation: Department of Biology, University of Alabama, Birmingham, AL, 35294, USA.
authors.forename: Travis
authors.initials: T
authors.lastname: Ptacek
authors.forename: Susan M
authors.initials: SM
authors.lastname: Sell
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics; D016208:Databases, Factual; D030541:Databases, Genetic; D005091:Exons; D016678:Genome; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D016753:Interleukin-10 / Q000378:metabolism; D007438:Introns; D051258:MafB Transcription Factor; D051379:Mice; D015513:Oncogene Proteins / Q000235:genetics; D012984:Software; D014157:Transcription Factors / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D004268:DNA-Binding Proteins; C490407:MAFB protein, human; D051258:MafB Transcription Factor; C490406:Mafb protein, mouse; D015513:Oncogene Proteins; D014157:Transcription Factors; D016753:Interleukin-10