Genomic data: datasets, analysis tools and other resources
Datasets
Arabidopsis thaliana 1001 genomes project.
TAGdb Searchable plant data for barley, wheat, Brassica spp., Nicotiana and Pongamia.
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Assembly
VELVET For short reads (454/Solexa)
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Structural annotation
Once assembled, genomic data can be annotated using traditional gene prediction tools. Depending on sequencing technology/depth, erros may perturbate gene prediction.
The gene prediction process can be fed using short-read RNA-seq data (either mapped directly or assembled and mapped as you would do with EST clusters).
