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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
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
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  . ...doi:10.4056/sigs.69.1277 pmid:21304682 pmcid:PMC3035250 fatcat:6nvkkusozvbz7ifhyu5v2v3gxe
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
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  , or sequencing cloned bridging PCR fragments with subcloning. ...doi:10.1186/1471-2164-12-235 pmid:21569405 pmcid:PMC3164228 fatcat:nyh7mzapvfc2pdn7d2pyc7hdom