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ClassyFire has been used to annotate over 77 million compounds and has already been integrated into other software packages to automatically generate textual descriptions for, and/or infer biological properties of over 100,000 compounds.
Recently, poly(A -position profiling by sequencing (3P-seq) A -positionimilar methods have successfully been used to annotate 3′ UTRs; however, they contain comprofilingbyochemical experimental sequencingulting in a low yield of products.
The tool has already been employed in the annotation of over 29,000 predicted gene sequences from the large scale Vitis vinifera sequencing project [28] and has been used to annotate a small subset of over 500 sequences from a cDNA-AFLP sequencing project in Medicago truncatula [29].
In addition, evolutionary sequence conservation information has been used to annotate all mutant sites.
Such an approach has been used to annotate unknown proteins in S. cerevisiae protein interaction networks [ 103].
These slims provide an overview of the specific terms that have been used to annotate a set of genes.
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Standard Illumina annotation was used to annotate methylation data.
Finally, the homolog annotations were used to annotate the uncharacterized genes.
The BLAST search interface can be used to annotate unknown sequences, or to investigate annotations in other databases.
The RAST annotation server [25] was used to annotate the plasmid genomes.
The Maker annotation pipeline [ 9] was used to annotate the A. apis genome [ 7].
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