title: COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for mining complex motifs in whole genomes.
abstract: BACKGROUND
  The complete sequencing of the human genome shows that only 1% of the entire genome encodes for proteins. The major part of the genome is made up of non-coding DNA, regulatory elements and junk DNA. Transcriptional regulation plays a central role in a multitude of critical cellular processes and responses, and it is a central force in the development and differentiation of multicellular organisms. Identifying regulatory elements is one of the major tasks in this challenge. To accomplish this task, we developed a solid and simple suite that allows direct access to genomic database and immediate result check. We introduce COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for motif search in entire genomes. Motifs can be partially degenerated and interrupted by spacers of variable length.
  
  
  RESULTS
  We demonstrate through real biological data mining the simplicity and robustness of this tool. The test was performed on two well-known protein domains and a highly variable cis-acting element. COMPASSS successfully identifies both protein domains and cis-acting semi-conserved elements.
  
  
  BACKGROUND
  The COMPASSS suite is available for Windows free of charge from our web sites: compasss.sourceforge.net/; www.stefanolandi.eu/
authors.affiliation: Laboratory of Microbiology and Genetics - Ospedale di Circolo e Fondazione Macchi, University of Insubria, Viale Borri 57 21100 Varese, Italy. gpmaccari@gmail.com
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Maccari
authors.forename: Federica
authors.initials: F
authors.lastname: Gemignani
authors.forename: Stefano
authors.initials: S
authors.lastname: Landi
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D057225:Data Mining / Q000379:methods*; D016678:Genome; D020407:Internet; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins