Although 56,797 genes have been annotated from sequencing of the rice genome [3], [4], the functions of >60% of these predicted genes are unknown.
The miRNA precursor sequence was annotated from deep sequencing reads using the miRDeep algorithm [ 48] optimized for plant miRNA [ 48].
In rice, 1,200 transporter proteins have been annotated from the genome sequence, among which 84% are active transporters (Nagata et al. 2008).
Approximately 39,441 protein coding transcripts were annotated from the whole genome sequence of sorghum (http://phytozome.jgi.doe.gov/).gov/
However, as both modules employ the traditional Top-BLAST approach, each query sequence is annotated from only one putative orthologue.
Repeat sequences were annotated from the SSB draft genome scaffolds using the RepeatMasker program version 3.0 with default parameters (20).
The finished assembled sequences were annotated from the Prokaryotic Genomes Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).html
The final finished genome sequences were annotated from the Prokaryotic Genomes Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).html
All miRNAs were annotated from pre-miRNA and mature miRNA sequences listed in the latest release of miRBase.
Proteins predicted to be encoded by the assemblies were annotated from the BLASTX reports comparing Triphysaria sequences to either all proteins in GenBank (rel145.fsa_aa release Dec 15 , 2004 or to all predicted proteins in Arabidopsis (ATH1.pep_cm_20040228).
