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Finally, the mutations predicted to change amino acids were analyzed by using the annotated version of Gmax_189.
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Experimental pairs were annotated using the annotated unigene transcriptome library.
Annotations with Gene Ontology (GO), Enzyme Commission (EC) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms were inferred for these proteins using annot8r (version 1.1.1) [ 37], using the annotated sequences available in uniref100 [ 34].
The probability of a feature vector is calculated with each label using the annotated training dataset.
It finds a separation among the data using the annotated training dataset.
Position of mutations overlapping with known gene annotations and those resulting in amino acid changes were searched by using amino acid changes annotation module against the annotated version of Gmax_189 obtained from Phytozome FTP site [ 67].
However, although GRASSIUS contains maize and rice TFs, it used the old annotated version of maize and rice genomes (v3b.50 for maize and TIGR5 for rice) for TF identification.
The annotated version of the C. glutamicum ATCC 13032 genome sequence [ 6] was used to perform a genome-wide screening for putative DtxR binding sites.
An improved annotation of these mapped genes will have to wait for the annotated version of the Eucalyptus grandis genome.
Since it came out last week, the annotated version (with an initial print run of just 4,000 copies) has had a success, with 15,000 copies ordered.
After a debate about government interference and scientific freedoms erupted, the Institute decided to publish the annotated version itself, in 2016.
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