This information resource contains the Orzya longistaminata reference genome V2.0.
Data sources:
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.
The gene models were constructed using in silico gene prediction by Megante (published here) in combination with gene models obtained from our RNAseq data (unpublished) using hisat2 and stringtie.
The genome browser is based on JBrowse described here. The blast server used the NCBI blast+ executables and the sequenceserver GUI described here.
The transcriptome datamining UIs and the sequence retrieval UI were made using R and shiny.
The development of this website was supported by CREST in the laboratory 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).
Since this is partially unpublished data we ask for fair use as specified in:
- Marshall E: Bermuda rules: community spirit, with teeth. Science. 2001, 291 (5507): 1192-10.1126/science.291.5507.1192.
- Sharing data from large-scale biological research projects: a system of tripartite responsibility. (Wellcome Trust, 2003)
- Toronto International Data Release Workshop Authors: Prepublication data sharing. Nature. 2009, 461 (7261): 168-170.
Especially we request that any genome-wide analyses or meta-genome analyses is only conducted with our explicit permission.
Contact:
reuscher"at"agr"dot"nagoya-u.ac.jp
This website was made using wordpress and uses a template from DevDm.com.