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In the case of Arabidopsis array sequences, 40% lacked BLAST results thus limiting annotation coverage to a maximum of 60%.
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One reason is that SG typically selects targets with less than 30% sequence identity to known structures [5] [10], which limits annotation through homology.
Such limitations are likely due to: 1) incomplete overlap between domain-based and protein-based modules; 2) limited annotation coverage associated with ECM proteins; and 3) biases in functional annotation schemes toward protein-based rather than domain-based annotations (Vogel et al. 2005).
Homosapiens were selected to limit annotations.
We concluded that our low stringency bovine set captured a majority of actual bidirectional promoters, but that limited annotations contributed false positive and false negative predictions.
EST-derived unigenes often represent partial gene sequences, thereby limiting gene annotation based only on protein-domain information.
Limiting the annotation to selected cell types may only be considered if extensive prior knowledge about the target cell and tissue type exists.
In this manner, we were able to identify a larger set of gene ontology annotations per feline gene than we could have accomplished if we limited the annotation mapping to only the feline cDNA sequences we identified.
However, we also found that the lack of genome sequence information may limit gene annotation, subsequently influencing in-depth mining and selection of candidate genes.
However, the use of lipidomics in higher plants has been limited to annotation of pathways [114] [116] and response to environmental stresses [117], with no direct application for biofuels so far.
The set of mostly noncoding transcripts located within heterochromatin regions therefore currently has limited GO annotation.
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