Abstract
Obtaining bacterial genomic sequences has become a routine task in today’s biology. The emergence of the comparative genomics approach has led to an increasing number of bacterial species having more than one strain sequenced, thus facilitating the annotation process. On the other hand, many genomic sequences are now left in the “draft” status, as a series of contigs, mainly for the labor-intensive finishing task. As a result, many genomic analyses are incomplete (e.g., in their annotation) or impossible to be performed (e.g., structural genomics analysis). Many approaches have been recently developed to facilitate the finishing process or at least to produce higher quality scaffolds; taking advantage of the comparative genomics paradigm, closely related genomes are used to align the contigs and determine their relative orientation, thus facilitating the finishing process, but also producing higher quality scaffolds.
In this chapter we present the use of the CONTIGuator algorithm, which aligns the contigs from a draft genome to a closely related closed genome and resolves their relative orientation based on this alignment, producing a scaffold and a series of PCR primer pairs for the finishing process. The CONTIGuator algorithm is also capable of handling multipartite genomes (i.e., genomes having chromosomes and other plasmids), univocally mapping contigs to the most similar replicon. The program also produces a series of contig maps that allow to perform structural genomics analysis on the draft genome. The functionalities of the web interface, as well as the command line version, are presented.
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References
Angiuoli S, Hotopp JD, Salzberg S, Tettelin H (2011) Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinformatics 12:272
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M (2009) ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 25:1968–1969
Camacho C, Coulouris G, Avagyan V et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421
Carver TJ, Rutherford KM, Berriman M et al (2005) ACT: the Artemis comparison tool. Bioinformatics 21:3422–3423
Compeau PE, Pevzner PA, Tesler G (2011) How to apply de Bruijn graphs to genome assembly. Nat Biotechnol 29:987–991
Dias Z, Dias U, Setubal JC (2012) SIS: a program to generate draft genome sequence scaffolds for prokaryotes. BMC Bioinformatics 13:96
Galardini M, Biondi EG, Bazzicalupo M, Mengoni A (2011) CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 6:1
Harrison PW, Lower RP, Kim NK, Young JPW (2010) Introducing the bacterial “chromid”: not a chromosome, not a plasmid. Trends Microbiol 18:141–148
Kurtz S, Phillippy A, Delcher AL et al (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15:589–594
Muñoz A, Zheng C, Zhu Q et al (2010) Scaffold filling, contig fusion and comparative gene order inference. BMC Bioinformatics 11:304
Richter DC, Schuster SC, Huson DH (2007) OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics 23:1573–1579
Rozen S, & Skaletsky H. (1999). Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics methods and protocols (pp. 365–386). Humana Press
Silva GG, Dutilh BE, Matthews TD et al (2013) Combining de novo and reference-guided assembly with scaffold_builder. Source Code Biol Med 8:23
Tettelin H, Riley D, Cattuto C, Medini D (2008) Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 11:472–477
van Hijum SA, Zomer AL, Kuipers OP, Kok J (2005) Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res 33:W560–W566
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Galardini, M., Mengoni, A., Bazzicalupo, M. (2015). Mapping Contigs Using CONTIGuator. In: Mengoni, A., Galardini, M., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 1231. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1720-4_11
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DOI: https://doi.org/10.1007/978-1-4939-1720-4_11
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1719-8
Online ISBN: 978-1-4939-1720-4
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