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http://dx.doi.org/10.5808/GI.2009.7.1.046

A Simple Java Sequence Alignment Editing Tool for Resolving Complex Repeat Regions  

Ham, Seong-Il (Department of Architectural Engineering, Yonsei University)
Lee, Kyung-Eun (Department of Computer Science, Ewha Womans University)
Park, Hyun-Seok (Institute of Bioinformatics, Macrogen Inc.)
Abstract
Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.
Keywords
fragment assembly; genome sequencing; whole genome fragment assembly;
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1 Bailey, J., et al., (2002). Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70, 83-100   DOI   ScienceOn
2 Myers, E.W., et al. (2000). A wholegenome assembly of Drosophila. Science 287, 2196-204   DOI   ScienceOn
3 She, X., et al. (2004). Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431, 927-930   DOI   ScienceOn
4 Arner, E., et al. (2006). DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions. BMC Bioinformatics 20, 155   DOI
5 Edwards, A., and Caskey, C.T. (1990). Closure strategies for random DNA sequencing methods. A Companion to Methods in Enzymology 3, 41-47   DOI
6 Eichler, E.E., Clark, R.A., and She, X. (2004). An assessment of the sequence gaps: unfinished business in a finished human genome. Nat Rev Genet. 5, 345-354   DOI   ScienceOn