title: Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.
abstract: BACKGROUND
  Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes.
  
  
  RESULTS
  We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at http://family.caltech.edu/.
  
  
  CONCLUSIONS
  These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.
authors.affiliation: Division of Biological Sciences, California Institute of Technology, Pasadena, CA 91125, USA. titus@caltech.edu
authors.forename: C Titus
authors.initials: CT
authors.lastname: Brown
authors.forename: Yuan
authors.initials: Y
authors.lastname: Xie
authors.forename: Eric H
authors.initials: EH
authors.lastname: Davidson
authors.forename: R Andrew
authors.initials: RA
authors.lastname: Cameron
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D005091:Exons; D005809:Genes, Regulator; D016678:Genome; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface