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However, the human genome is well annotated with abundant EST evidence, allowing evaluation of HMMSplicer's performance on transcripts with low abundance, alternatively spliced junctions, and non-canonical junctions.
C. elegans and D. melanogaster are likely to be the best candidates to directly apply this approach, because their genomes are well annotated with whole genome tiling array and EST data [138] [140].
All the phosphoproteins were well annotated with various descriptions and the source references for phosphorylation identifications were also provided.
However, a limitation is that candidate proteins need to be well annotated with a sufficient number of GO terms.
The data present in dbEST is not well annotated with regard to the precise origin of the source tissue used in cDNA library construction.
Proteogenomic mapping indicates that the current M. hyopneumoniae strain 232 genome is well annotated with only 1.8% of peptide mappings not belonging to currently known genes.
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Of the total number of annotated transcripts, 17,788 transcripts were well annotated (assigned with a gene name as well as a protein signature), obtained from union of BLASTX and InterProScan annotated transcripts, detailed in Figure 1C.
Four well annotated genes with a fiber initiation-specific pattern of expression give potentially new insight into fiber initiation.
Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20.
Furthermore, the ability to apply molecular quantification techniques to FFPE samples introduces the possibility of conducting large retrospective validation studies for new molecular diagnostics on well annotated samples with long-term follow-up.
There was no question that the value of the Celera sequence, however well annotated, would decrease with time.
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