taxutils: Tools for managing and operating on NCBI taxonomy and accession mappings
O'Brien, W.; Lee, S.; Agarwal, V.; Eskin, E.
Show abstract
Research in bioinformatics demands that many workflows and operations be consistently repeated across different tools. These operations include managing a taxdump, dealing with accession mappings, and performing analysis on the taxonomic tree. We introduce taxutils to address and alleviate the strain of these common workflows. To exhibit the extent of the package's capabilities, we introduce a strategy for assessing quality of an assembly via its potential impact on and perturbation of its mapping to a lowest-common-ancestor index. We illustrate the steps required for such an analysis, and show how the tool makes data management easy and otherwise-complex workflows simple.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.