OSLay: Optimal syntenic layout of unfinished assemblies

Bioinformatics

Volumn 23, Issue 13, 2007, Pages 1573-1579

  Richter, Daniel C ^a   Schuster, Stephan C ^b   Huson, Daniel H ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG;

ACCESS TO INFORMATION; COMPUTER PROGRAM; CONFERENCE PAPER; CONTROLLED STUDY; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; INTERNET; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SYNTENY;

EID: 34547852218     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm153     Document Type: Conference Paper

References (19)

1. Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Bartels, D. et al. (2005) BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics, 21, 853-859.
3. Delgado-Friedrichs, O. et al. (2003) A recta-viewer for biomolecular data. GI Jahrestagung, 1, 375-380.
4. Frangeul, L. et al. (2004) CAAT-Box, Contigs-Assembly and Annotation Tool-Box for genome sequencing projects. Bioinformatics 20, 790-797.
5. Friedrichs, O. et al. (2004) Syntenic Layout of Two Related Genomes. Proceedings of GCB 2004.
6. Gabow, H. (1976) An efficient implementation of Edmond's algorithm for maximum matching on graphs. J. ACM, 23, 221-234.
7. Garey, M.R. and Johnson, D.S. (1979) Computers and Intractability: A guide to the theory of NP-completeness. W. H. Freeman and Company. New York, NY, USA.
8. Gordon, D. et al. (1998) Consed: A graphical tool for sequence finishing. Genome Res., 8, 195-202.
9. Kurtz, S. et al. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
10. Margulies, M. et al. (2005) Genome sequencing in microfabrieated high-density picolitre reactors. Nature, 437, 367-380.
11. Myers, E.W. (1999) Whole-genome DNA sequencing. IEEE Comput. Eng. Sci., 3, 33-43.
12. Rendulic, S. et al. (2004) A predator unmasked: Life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science, 303, 689-692.
13. Sanger, F. et al. (1977) DNA sequencing with chain-terminating inhibitors. Biotechnology, 24, 104-108.
14. Sanger, F. et al. (1982) Nucleotide sequence of bacteriophage λ DNA. J. Mol. Biol., 162, 729-773.
15. Smit, A.F.A. et al. (1996-2004) RepeatMasker Open-3.0.
16. van Hijum, S. et al. (2005) Projector2: Contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res., 33, 560-566.
17. Velicer, G.J. et al. (2006) Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc. Natl Acad. Sci. USA, 103, 8107-8112.
18. Xu, J. and Gordon, J.I. (2005) MapLinker: A software tool that aids physical map-linked whole genome shotgun assembly. Bioinformatics, 21, 1265-1266.
19. Yu, Z. et al. (2005) PGAAS: A prokaryotic genome assembly assistant system. Bioinformatics, 18, 661-665.