We demonstrate the feasibility of converting the abundant manual annotations in biomedical databases into labeled instances that can be readily used by supervised machine-learning algorithms.
Expanded gene families in all 3 species were abundant in proteins with similar Pfam annotations.
Errors in annotation are particularly abundant in large, high G + C content genomes, where gene length and gene organization vary significantly from well-annotated model organisms such as Escherichia coli, Saccharomyces cerevisiae or Bacillus subtilis.
However, certain InterPro annotations were more abundant in the An.
His progressive outlook and bold innovations are confirmed in surviving fragments of his works and in the abundant citations and annotations of them by subsequent Roman jurists.
A provisional solution has been to focus manual annotation on those organisms that are abundant in a particular habitat, i.e. the Human Oral Microbiome Database (HOMD) (15).
The GO annotation showed that genes involved in metabolic processes were less abundant in the enriched library than in the control (30% versus 64% of all annotated contigs in the enriched and control libraries, respectively).
Again, genes with a functional annotation tag of that type were less abundant in the up-regulated gene set and enriched in the down-regulated gene set.
Moreover, Xia et al. also applied this classifier onto the whole KOME database (Knowledge-based Oryza Molecular Biological Encyclopedia, ftp://cdna01.dna.affrc.go.jp/pub/data//20081001/20081001/INE_FULL_SEQUENCE_DB_20081001.zip) and located the top 10 candidate genes, most of which own abundant annotation information in conserved domain information.
Gene ontology (GO) analyses16 using fruit fly, which has extensive GO annotations, indicate that HG derived from the first animal genome were abundant in protein classes implicated in gene regulation (e.g., nucleic acid binding, transcription factors) and catalytic activities (e.g., hydrolases, transferases, and oxidoreductases; Supplementary Data 4).
GH61s, i.e. members of the Glycoside Hydrolase family 61, are almost exclusively found in fungi (two annotations in the maize genome form the only exception) and are often abundant in wood degrading fungi.
