Abstract
BackgroundThe NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification.ResultsIn this paper, we present a solution to the problem of generating modifications of the NCBI taxonomy, based on the computation of an edit script that summarises the differences between two classification trees. Our algorithms find the shortest possible edit script based on the identification of all shared subtrees, and only take time quasi linear in the size of the trees because classification trees have unique node labels.ConclusionThese algorithms have been recently implemented, and the software is freely available for download from .
Highlights
The National Center for Biotechnology Information (NCBI) taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification
Every sequence in GenBank is associated with a taxon, and each taxon has a unique place in the NCBI taxonomy
A user downloads the NCBI taxonomy tree, edits the tree to reflect their preferred classification
Summary
The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. The NCBI Taxonomy [1] provides one of the most powerful ways to navigate the National Center for Biotechnology Information (NCBI) sequence data bases. In this classification, the Bilateria are split into three groups (Acoelomata, Pseudocoelomata, and Coelomata) based on the nature of the internal body cavity (coelom). The Coelomata are themselves split into two groups, the Protostomia and the Deuterostomia, characterised by the fate of the blastopore during development (in the Protostomia this becomes the mouth, in the Deuterostomia it becomes the anus)
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