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These 3 sets of target genes were imported into the Ingenuity Pathway Analysis (IPA) tool to identify biological activities based upon the underlying literature derived annotation.
The annotation file contains accession numbers, source clone name, and source assigned annotation or Blast derived annotation.
For instance, manual curation promises greater quality than computationally derived annotation, but its coverage is often inferior.
Once the maize genome has been computationally annotated using both de novo and comparative methods, instances of genes where cDNA and/or mRNA evidence are not congruent with the computationally derived annotation will be identified.
Users can, for example, find all ESTs associated with a particular GO term, run BLAST queries against the sequences in the database, view contigs and chromatograms, and view BLAST derived annotation.
We also included a derived annotation as an approximation for a negative control: From the intergenic dataset we excluded sites overlapping with any form of evolutionary, regulatory or genic annotation examined here, so that it is negative for sequence annotation irrespective of epigenetic state.
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"Collects NMR data from any experiment and captures assigned chemical shifts, coupling constants, and peak lists for a variety of macromolecules; contains derived annotations such as hydrogen exchange rates, pKa values, and relaxation parameters".--World Wide Protein Data Bank member page.
The Venn diagrams shown in Fig. 7 illustrate the overlap between CID-PMID associations provided by depositors and derived annotations via MeSH.
Strong evidence of particular features leading to accurate gene/term associations may lead to the establishment of empirically derived annotation-transfer rules.
Only experimentally derived annotations or annotations generated using sequence orthologs were used, leaving 132 (9%) of genes unannotated (Table 1).
The genomes may be "complete" or they may be in hundreds of contigs (which does impact the quality of the derived annotations).
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