Mauve: multiple alignment of conserved genomic sequence with rearrangements. As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under consideration. Furthermore, the linear order of these segments may be shuffled among genomes. We present methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer. Our methods have been implemented in a software package called Mauve. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.

References in zbMATH (referenced in 16 articles )

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  1. Shieh, Yi-Kung; Shyu, Shyong Jian; Lu, Chin Lung; Lee, Richard Chia-Tung: The exact multiple pattern matching problem solved by a reference tree approach (2021)
  2. Clark, Chad; Egri-Nagy, Attila; Francis, Andrew; Gebhardt, Volker: Bacterial phylogeny in the Cayley graph (2019)
  3. Tao, Jin; Liu, Xiaoqing; Yang, Siqian; Bao, Chaohui; He, Pingan; Dai, Qi: An efficient genomic signature ranking method for genomic island prediction from a single genome (2019)
  4. Bhatia, Sangeeta; Feijão, Pedro; Francis, Andrew R.: Position and content paradigms in genome rearrangements: the wild and crazy world of permutations in genomics (2018)
  5. DeBlasio, Dan; Kececioglu, John: Parameter advising for multiple sequence alignment (2017)
  6. Egri-Nagy, Attila; Gebhardt, Volker; Tanaka, Mark M.; Francis, Andrew R.: Group-theoretic models of the inversion process in bacterial genomes (2014)
  7. Braga, Marília D. V.; Chauve, Cedric; Doerr, Daniel; Jahn, Katharina; Stoye, Jens; Thévenin, Annelyse; et al.: The potential of family-free genome comparison (2013)
  8. Warnow, Tandy: Large-scale multiple sequence alignment and phylogeny estimation (2013)
  9. Elloumi, Mourad (ed.); Zomaya, Albert Y. (ed.): Algorithms in computational molecular biology. Techniques approaches and applications. (2011)
  10. Herbig, Alexander; Nieselt, Kay: Nocornac: characterization of non-coding rnas in prokaryotes (2011) ioport
  11. Palmer, Lance E.; Dejori, Mathäus; Bolanos, Randall A.; Fasulo, Daniel P.: Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction (2010) ioport
  12. Rissman, Anna I.; Mau, Bob; Biehl, Bryan S.; Darling, Aaron E.; Glasner, Jeremy D.; Perna, Nicole T.: Reordering contigs of draft genomes using the mauve aligner (2009) ioport
  13. Swidan, Firas; Shamir, Ron: Assessing the quality of whole genome alignments in bacteria (2009) ioport
  14. Tsafnat, Guy; Coiera, Enrico W.; Partridge, Sally R.; Schaeffer, Jaron; Iredell, Jon R.: Context-driven discovery of gene cassettes in mobile integrons using a computational grammar (2009) ioport
  15. Doring, Andreas; Weese, David; Rausch, Tobias; Reinert, Knut: Seqan - an efficient, generic C++ library for sequence analysis (2008) ioport
  16. Lemaitre, Claire; Sagot, Marie-France: A small trip in the untranquil world of genomes: a survey on the detection and analysis of genome rearrangement breakpoints (2008)