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The decision process involved in making annotations using PAINT is shown in Figure 4. Step 1 is to determine which ancestor would be annotated based on the experiment-based annotations to a given term, or its related terms in the ontology.
In total 38,535 transcripts (89.9 %) could be annotated based on similarity to annotated genes in either the chicken or zebra finch.
A total of 2452 genes (25.3% of all gene sequences) could not be annotated based on matches in the NCBI database (the full annotations of M. fructicola unigenes is found in Additional file 2).
Here, an a-ion at m/z 221 confirmed the sequence Ala-Hty, and most of the peaks of the tandem mass spectrum could be annotated based on the postulated sequence.
Proteins which could be annotated based on their 3D folds included ClpB, Hcp, VgrG, VasF, VCA0109, VCA0112, VCA0119 and VCA0121.
Approximately 50% of the unigenes could be annotated based on homology matches in the NCBI database.
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Identified SNP locations were annotated based on UCSC annotation databases and dbSNP using annovar annotation software [ 56].
Both tools were trained on scientific abstracts, but the training corpora comprise different articles and were annotated based on different annotation guidelines [31].
All methylated genes were annotated based on GO annotation.
The DETs were annotated based on NetAffx annotation data for cotton GeneChip (http://www.affymetrix.com).
Only the tags displaying zero or one mismatch were annotated based on the reference genes.
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