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Using the full database for each trait, we obtained haplotype mappings which were correlated in a manner that echoed the phenotype correlation; this practice has limitations in that it can mask important loci.
Our method using the full database could not assign species-specific labels to 25.8% of the reads; 8.5% of the reads were assigned labels with ranks at the genus, family and order levels; 6.9% and 3.1% of the reads not listed in Table 1 were correctly assigned labels at other ranks (e.g. kingdom, sub-species, class etc).
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More generally, we found, using the full STRING database, that those links which overlapped between CODA and any of the other fusion methods tended to have evidence from other types of prediction methods, most often gene neighbourhood.
Outputs were compared to conventional PRR calculations using the full EV database background.
Using the full NTP database, the prediction accuracy of Progol was estimated to be 63% (+/- 3%) using 5-fold cross validation.
PFAM analysis was conducted using an HMM-based search (CLC Genomics version 7.0) of all MAKER-derived protein models using the full PFAM database (version 22.0).
Reads passing strict mapping were next analyzed with MALT using the full NCBI nucleotide database as a reference to ensure proper assignment to Homo sapiens rather than to other organisms.
Additional testing of the model approach using the full Acadian Forest database is required, but will also require substantial increases in computational resources.
These models were screened using the full human genome and databases of promoter sequences from human and several other mammalian species.
For example, if the ChEMBL web application is running on the user's local machine, e.g. http://localhost:8080/chembl/, then a request for the article with identifier "a31863", http://localhost:8080/chembl/article/a31863, will be resolved using the webapp from the database using the full original URI, http://linkedchemistry.info/chembl/activity/a31863.info/chembl/activity/a31863
We identify mutations in the promoter and coding regions of the candidate regulators using the full genome sequences available from public databases to provide strong evidence that the candidate regulators are true regulators.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com