PMC:3091627 / 30726-32250
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3091627","sourcedb":"PMC","sourceid":"3091627","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091627","text":"Sequence data base calling was carried out using Phred [40]. Sequences not meeting our production quality criteria (at least 100 bases called with a quality over 20) were discarded. Sequences were screened against plasmid vector and E. coli sequences. The traces were assembled using Phrap and Consed [41]. Whole genome shotgun sequencing was performed to ensure approximately 11-fold coverage. Autofinish [42] was used to design primers for improving regions of low quality sequence and for primer walking along templates spanning the gaps between contigs. Several strategies were used to orientate contigs and to enable directed PCR-based approaches to span the gaps between contigs. These strategies included linking isolates and a Blast-based approach, which identified contigs with hits to the H. pylori strain 26695 genome. Various combined PCR techniques were used to amplify genomic or cosmid DNA, to close the gaps between the final contigs. Outward-directed primers were designed for each of the contig ends; the primer sequences were subsequently checked and confirmed to be unique to the genome. This combined PCR process required approximately 200 PCR reactions pairing each of the primers. In addition, two cosmid isolates containing a rDNA operon copy each, were completely sequenced by sub-cloning into a pSMART-LC vector (Lucigen Corp.). The error rate was less than 1 error per 10,000 bp in the final assembly. The complete genome sequence was obtained from 40 153 sequences, resulting in 14-fold coverage.","tracks":[{"project":"2_test","denotations":[{"id":"20537153-9521922-10781753","span":{"begin":56,"end":58},"obj":"9521922"},{"id":"20537153-9521923-10781754","span":{"begin":302,"end":304},"obj":"9521923"},{"id":"20537153-11282977-10781755","span":{"begin":407,"end":409},"obj":"11282977"}],"attributes":[{"subj":"20537153-9521922-10781753","pred":"source","obj":"2_test"},{"subj":"20537153-9521923-10781754","pred":"source","obj":"2_test"},{"subj":"20537153-11282977-10781755","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ecbd","default":true}]}]}}