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Future work will be dedicated to the improvement of the clustering step in the TEdenovo pipeline in order to provide, also to very large genomes, the ability to jointly annotate TEs and study their diversification.
Results: Using the annotation of gene expression patterns across stages of Drosophila embryonic development as an example, we demonstrate that our method achieves superior accuracy, gained by jointly annotating phenotype sequences, when compared with previous models that annotate each stage in isolation.
Phenotypes are typically annotated stage-by-stage, without jointly learning the salient temporal dependencies across multiple time points, which should allow for an overall higher accuracy; e.g. the annotation terms predicted for earlier stages should inform the prediction at later stages.
Single nucleotide variants and indels were jointly called within each trio using the GATK HaplotypeCaller and annotated using SnpEff v3.3 and SnpSift (Cingolani et al., 2012).
For each promoter sequence, we pair different TFs that have annotated binding sites on it and consider these TF pairs to jointly regulate a given gene.
meticulously annotated.
Annotated copy.
(c) Annotated gene trees.
R.V.B. annotated reference genomes.
Using Genius, I annotated it.
I annotated it using Genius.
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