title: CoCoNUT: an efficient system for the comparison and analysis of genomes.
abstract: BACKGROUND
  Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons.
  
  
  RESULTS
  Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping cDNA/EST to genomic sequences.
  
  
  CONCLUSIONS
  CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component), CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics.
authors.affiliation: Faculty of Engineering, Cairo University, Giza, Egypt. mabouelhoda@yahoo.com
authors.forename: Mohamed I
authors.initials: MI
authors.lastname: Abouelhoda
authors.forename: Stefan
authors.initials: S
authors.lastname: Kurtz
authors.forename: Enno
authors.initials: E
authors.lastname: Ohlebusch
mesh_terms: D000818:Animals; D055028:Comparative Genomic Hybridization / Q000379:methods*; D006801:Humans; D012984:Software / Q000639:trends; D013223:Statistics as Topic / Q000379:methods* / Q000639:trends