PMC:3514855 / 6933-7981 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3514855","sourcedb":"PMC","sourceid":"3514855","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3514855","text":"Sequencing of genomic DNA was carried out on an Illumina Genome Analyzer IIx system. Prior to sequencing, the DNA was sheared by ultrasonication (Covaris, Woburn, MA, USA), resulting in fragments of 300 bp length on average. For these fragments paired-end sequencing according to the manufacturer's protocol was carried out, resulting in 42 143 495 million 101 nt long reads. These reads were analysed with two methods in order to identify SNPs, deletions and insertions. For the first approach, we used the DNA sequence data assembler algorithm MIRA (Mimicking Intelligent Read Assembly)18 to perform an assembly of the reads using the ‘GT-Kazusa’ genome as the reference. In the assembly process, MIRA generates tables of candidate SNPs, insertions and deletions. We verified these results independently by mapping all sequencing reads to the assembled chromosome and plasmid sequences. This was done using segemehl,19 requiring at least 85% accuracy and reporting only the best hit. It should be noted that segemehl reports co-optimal best hits.","tracks":[{"project":"2_test","denotations":[{"id":"23069868-19750212-25970076","span":{"begin":918,"end":920},"obj":"19750212"}],"attributes":[{"subj":"23069868-19750212-25970076","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#b6ec93","default":true}]}]}}