Evaluating synteny for improved comparative studies

Bioinformatics

Volumn 30, Issue 12, 2014, Pages

  Ghiurcuta, Cristina G ^a   Moret, Bernard M E ^a  

^a EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; FUNGAL GENOME; GENETICS; GENOMICS; METHODOLOGY; SEQUENCE ALIGNMENT; SYNTENY; YEAST;

GENOME, FUNGAL; GENOMICS; SEQUENCE ALIGNMENT; SOFTWARE; SYNTENY; YEASTS;

EID: 84902506954     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu259     Document Type: Article

References (27)

1. Altschul, S. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Baudet, C. et al. (2010) Cassis: Detection of genomic rearrangement breakpoints. Bioinformatics, 26, 1897-1898.
3. Bergeron, A. (2002) Common intervals and sorting by reversals: a marriage of necessity. Bioinformatics, 18, S54-S63.
4. Bourque, G. et al. (2004) Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res., 14, 507-516.
5. Byrne, K. and Wolfe, K. (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res., 15, 1456-1461.
6. Calabrese, P. et al. (2003 Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics, 19 (Suppl 1), i74-i80.
7. Compeau, P. et al. (2011) How to apply de Bruijn graphs to genome assembly. Nat. Biotech., 29, 987-991.
8. Darling, A. et al. (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One, 5, e11147.
9. Deonier, R. et al. (2005) Computational Genome Analysis: An Introduction. SpringerVerlag, Berlin.
10. Fitch, W. (2000) Homology: a personal view on some of the problems. Trends Genet., 16, 227-231.
11. Fu, Z. et al. (2007) MSOAR: a high-throughput ortholog assignment system based on genome rearrangement. J. Comput. Biol., 14, 1160-1175.
12. Gabaldon, T. and Koonin, E. (2013) Functional and evolutionary implications of gene orthology. Nat. Rev. Genet., 14, 360-366.
13. Jahn, K. (2011) Efficient computation of approximate gene clusters based on reference occurrences. J. Comput. Biol., 18, 1255-1274.
14. Krzywinski, M. et al. (2009) Circos: an information aesthetic for comparative gen-omics. Genome Res., 19, 1639-1645.
15. Minkin, I. et al. (2013) Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes. In Proceedings of the 13th Workshop Algorithms in Bioinformatics (WABI'13), Vol. 8126 of Lecture Notes in Computer Science, pp. 215-229. Springer Verlag, Berlin.
16. Nadeau, J. and Taylor, B. (1984) Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl Acad. Sci. USA, 81, 814-818.
17. Paten, B. et al. (2009) Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics, 25, 295-301.
18. Pearson, W. (1998) Empirical statistical estimates for sequence similarity searches. J. Mol. Biol., 276, 71-84.
19. Pevzner, P. and Tesler, G. (2003) Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res., 13, 37-45.
20. Pham, S. and Pevzner, P. (2010) DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics, 26, 2509-2516.
21. Proost, S. et al. (2012) i-ADHoRe 3.0-fast and sensitive detection of genomic hom-ology in extremely large data sets. Nucleic Acids Res., 40, e11.
22. Renwick, J.H. (1971) The mapping of human chromosomes. Ann. Rev. Gen., 5, 81-120.
23. Roedelsperger, C. and Dieterich, C. (2010) CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. PLoS One, 5, e8861.
24. The Mouse Genome Sequencing Consortium. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
25. Vandepoele, K. et al. (2002) The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res., 12, 1792-1801.
26. Waterhouse, R. et al. (2011) OrthoDB: the hierarchical catalog of eukaryotic ortho-logs in 2011. Nucleic Acids Res., 39, D283-D288.
27. Zeng, X. et al. (2008) Orthocluster: A new tool for mining synteny blocks and applications in comparative genomics. In Proceedings of the 11th Conference of Extending Database Technology EDBT'08, pp. 656-667. ACM Press, New York.