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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
CoCoNUT: An efficient system for the comparison and analysis of genomes
BMC Bioinformatics, Volume 9, Article 476, Year 2008
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Description
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. 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 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. © 2008 Abouelhoda et al; licensee BioMed Central Ltd.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3224568/bin/1471-2105-9-476-S1.pdf
Authors & Co-Authors
Abouelhoda, Mohamed Ibrahim
Egypt, Cairo
Faculty of Engineering
Egypt, 6th October
Nile University
Kurtz, Stefan
Germany, Hamburg
Universität Hamburg
Ohlebusch, Enno
Germany, Ulm
Universität Ulm
Statistics
Citations: 23
Authors: 3
Affiliations: 4
Identifiers
Doi:
10.1186/1471-2105-9-476
e-ISSN:
14712105
Research Areas
Cancer
Genetics And Genomics