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Similarly, RAP-DB offers many annotations for japonica genome [ 16], while indica annotation is not presented.
Although RefSeq does contain manually curated genomes for some organisms, many annotations for bacterial genomes are listed as "provisional", meaning that they have not yet undergone final review by NCBI staff.
T. vaginalis had many annotations for its rRNAs and tRNAs and the majority were found by both contig and sequence (results are summarized in Additional file 1, Tables s1-s3).
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Then the penny dropped: it was my simplistic shorthand and too many annotations of m'd.
By contrast, many annotation methods, for instance the nearest-neighbor and BLAST approaches we benchmark against, do not make use of this information.
To account for the many annotations tested, we considered tests with expected FDR < 0.05 significant.
"You will not be vanquished although you are a man," reads one of many annotations that litter her work.
Furthermore, many annotations are ambiguous e.g.g
However, there are twice as many GO annotations for rat than currently exist for chicken and fewer of these annotations are IEA.
As many RefSeq annotations for prokaryotic genomes are largely based on the genomes' GenBank annotations when provided [ 14], the RefSeq annotations may still be missing large numbers of genes.
Annotation of left aligned data, as performed by many annotation tools, would thus give clinically discrepant annotation for the 339 (46 %) indels in genes transcribed from the forward DNA strand.
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