{"id":16,"date":"2016-10-29T15:34:22","date_gmt":"2016-10-29T06:34:22","guid":{"rendered":"http:\/\/localhost\/?page_id=16"},"modified":"2018-02-19T13:50:25","modified_gmt":"2018-02-19T04:50:25","slug":"about","status":"publish","type":"page","link":"http:\/\/133.39.75.173\/?page_id=16","title":{"rendered":"About"},"content":{"rendered":"
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This information resource contains the Orzya longistaminata reference genome V2.0.<\/p>\n

Data sources:<\/h4>\n

The genome sequence is derived from DNA extracted from the Oryza longistaminata accession IRGC110404 sequenced by SMRT technology and constructed using Falcon, quiver, pilon and ALLMAPS.<\/p>\n

The gene models were constructed using\u00a0in silico<\/em> gene prediction by Megante<\/a>\u00a0(published here<\/a>) in combination with gene models obtained from our RNAseq data (unpublished) using hisat2 and stringtie.<\/p>\n

The genome browser is based on\u00a0JBrowse<\/a>\u00a0described\u00a0here<\/a>. The blast server used the\u00a0 NCBI blast+ executables<\/a>\u00a0and the sequenceserver<\/a>\u00a0GUI described\u00a0here<\/a>.<\/p>\n

The transcriptome datamining UIs and the sequence retrieval UI were made using R and shiny<\/a>.<\/p>\n

The development of this website was supported by CREST<\/a> in the laboratory <\/a>of Motoyuki Ashikari. The main authors responsible are Stefan Reuscher and Tomoyuki Furuta, with contributions from Michele Cosi (genome browser) and Kanako Uehara (tissue transcriptome).<\/p>\n

Since this is partially unpublished data we ask for fair use as specified in:<\/p>\n