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I annotated only six other Drosophila genomes in addition to D. melanogaster (D. annasae, D. pseudoobscura, D. willistoni, D. mojavensis, D. virilis, and D. grimshawi) because this number well represents the phylogenetic diversity of sequenced Drosophila (Fig. 1).
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M12 obtained higher specificity (0.97) since it annotates only using very similar sequences (Fig. 4).
All proteins not included in a child GO term (i. e. annotated only with the parent GO term) were excluded from the cluster analyses.
Any sites with multiple transcripts resulting in multiple annotations were annotated only once using the by-gene option in VEP [ 35].
However, these analyses differed because the test corpus was annotated only for false negatives (i.e., missed PHI) and full human consensus annotations are only available for the gold standard corpus.
For each uncharacterized sequence, GO annotated (only non-electronic annotations) homologues are retrieved from the SIMAP sequence similarity matrix.
However, until recently SMIM1 was annotated only as a hypothetical protein (i.e. LOC388588) and thus SMIM1 may not have been present in exome arrays.
All unique annotated transcripts (15,385; see Results), excluding those annotated only with Unigene (2,549), were employed for microarray design.
However, a significant fraction mapped to sequences annotated only as introns (8%) and to regions without annotated genes (intergenic; 6%).
Variability was annotated only twice, however we do believe that it is an integral part of big data.
For the analysis of overlap between small RNAs or predicted hairpins and protein coding mRNAs, we excluded Affy transcripts annotated only as miRNAs, transcripts mapping to the mitochondrial genome, chromosome Y and transcripts missing gene ID annotations.
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