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Current Release: OMAP Short Arm (AA genome type)
A minimum tiling path of BAC clones (Amiraju et al. 2006) was selected across the short arm of chromosome 3 of Oryza nivara using a heavily manually edited physical map (Kim et al. 2008). The BACs were divided into six 3Mb pools and Roche GSFLX sequenced (Titanium and paired-end reads) to a depth of 18X. Sequence reads were assembled with Newbler (454) and Bambus (Pop et al. 2004i), followed by manual inspection of the assembly (Rounsley et al. 2009). The assembly resulted in a total of 527 scaffolds with a scaffold N50 of 55,790bp.
Additional annotations generated by the Gramene project include:
- Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see more.
- Identification of various repeat features from MIPS and AGI repeat libraries
- Ab initio gene prediction with program fgenesh
- Pairwise Whole genome alignments (blastz-chain-net) with Oryza sativa Japonica
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