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An algorithm for automated closure during assembly

Sergey Koren, Jason R Miller, Brian P Walenz, Granger Sutton
2010 BMC Bioinformatics  
Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local re-assembly of gap regions.  ...  Results: A procedure called the bounding read algorithm was developed for assembly of shotgun reads plus finishing reads and their constraints, targeting repeat regions.  ...  JRM assisted with test design and manuscript revision. BPW participated in the software development. GS proposed the project and reviewed its progress.  ... 
doi:10.1186/1471-2105-11-457 pmid:20831800 pmcid:PMC2945939 fatcat:k2uw2ijpavfbxio2lfnohqx25a

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)

Konstantinos Mavromatis, Johannes Sikorski, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin (+27 others)
2010 Standards in Genomic Sciences  
A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage.  ...  The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.  ...  A total of 767 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence.  ... 
doi:10.4056/sigs.591104 pmid:21304673 pmcid:PMC3035248 fatcat:qtzgw6ug55ephgs3g5o76qf3w4

Complete genome sequence of Haliangium ochraceum type strain (SMP-2T)

Natalia Ivanova, Chris Daum, Elke Lang, Birte Abt, Markus Kopitz, Elizabeth Saunders, Alla Lapidus, Susan Lucas, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Alex Copeland (+24 others)
2010 Standards in Genomic Sciences  
A total of 2,013 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence.  ...  Possible mis-assemblies were corrected with Dupfinisher or transposon bombing of bridging clones [31] .  ... 
doi:10.4056/sigs.69.1277 pmid:21304682 pmcid:PMC3035250 fatcat:6nvkkusozvbz7ifhyu5v2v3gxe

The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes

D. L. Maeder, I. Anderson, T. S. Brettin, D. C. Bruce, P. Gilna, C. S. Han, A. Lapidus, W. W. Metcalf, E. Saunders, R. Tapia, K. R. Sowers
2006 Journal of Bacteriology  
The genome of M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcina spp. in the region proximal to the origin of replication, with interspecies  ...  We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei.  ...  The immediately adjacent upstream region of the plasmid DNA contains a 5.6-kb noncoding region (15.3% of the plasmid sequence) characterized by a highly repetitive sequence consisting of over 38 direct  ... 
doi:10.1128/jb.00810-06 pmid:16980466 pmcid:PMC1636319 fatcat:mti5k2eg3rcv7cdevf5x2pj64a

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

Marco Galardini, Alessio Mengoni, Matteo Brilli, Francesco Pini, Antonella Fioravanti, Susan Lucas, Alla Lapidus, Jan-Fang Cheng, Lynne Goodwin, Samuel Pitluck, Miriam Land, Loren Hauser (+12 others)
2011 BMC Genomics  
Results: With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021.  ...  An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth.  ...  Possible mis-assemblies were corrected using gapResolution (Cliff Han, unpublished), Dupfinisher [56] , or sequencing cloned bridging PCR fragments with subcloning.  ... 
doi:10.1186/1471-2164-12-235 pmid:21569405 pmcid:PMC3164228 fatcat:nyh7mzapvfc2pdn7d2pyc7hdom