PMC:3746430 / 7650-8529 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3746430","sourcedb":"PMC","sourceid":"3746430","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3746430","text":"Genome sequencing and assembly\nThe random shotgun method was used in sequencing the genome of H. halophila SL1. Large (40 kb), median (8 kb) and small (3 kb) insert random sequencing libraries were sequenced for this genome project with an average success rate of 88% and average high-quality read lengths of 750 nucleotides. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher (unpublished, C. Han) or by transposon bombing of bridging clones (EZ-Tn5 \u003cP6Kyori/KAN-2\u003e Tnp Transposome kit, Epicentre Biotechnologies). Gaps between contigs were closed by editing, custom primer walks or PCR amplification. The completed genome sequence of H. halophila SL1 contains 36,035 reads, achieving an average of 12-fold sequence coverage per base with error rate less than 1 in 100,000.","divisions":[{"label":"Title","span":{"begin":0,"end":30}}],"tracks":[{"project":"MicrobeTaxon","denotations":[{"id":"T58","span":{"begin":94,"end":110},"obj":"349124"},{"id":"T59","span":{"begin":741,"end":757},"obj":"349124"}],"namespaces":[{"prefix":"_base","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"attributes":[{"subj":"T58","pred":"source","obj":"MicrobeTaxon"},{"subj":"T59","pred":"source","obj":"MicrobeTaxon"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"MicrobeTaxon","color":"#eca293","default":true}]}]}}