CoCoNUT: an efficient system for the comparison and analysis of genomes

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 to solve several different tasks in a unified framework: (1) finding syntenic regions (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. Conclusion: 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 ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch
• Keywords: BMCBI 2008, Comparative Genomics, Genomes, Software Tool