Conserved Domain
Database Debuts with
RPS-BLAST Search
Interface
Enhanced Access to
Taxonomy Database
Catch the Gene
Expression Omnibus
A Pair of Pathogens
Added to GenBank
Protein Molecular
Weight Field
Now in Entrez
OMIM In Entrez:
New Searching Power
Web Server
Software Available
for BLAST
Enhanced Access to Taxonomy Database
Several new search and display features enhance the utility of the NCBI Taxonomy database, which has also become a formal component of the Entrez set of integrated databases. Date-bounded queries are now supported, allowing users to identify all species that have been added since a particular date. A search option allows a phonetic spelling, such as “zenopis”, of an organism name, then presents a list of candidates from which the correct spelling, “xenopus”, can be chosen. Another convenient feature is a direct link from the Taxonomy home page to organisms commonly used in molecular research projects, such as H. sapiens, A. thaliana, and P. falciparum.
The NCBI taxonomic tree contains more than 79,000 taxa. To simplify the display of the hierarchy, a Common Subtree feature has been implemented, allowing users to build a custom phylogenetic tree for selected taxa. With this tool, users can add or delete taxa, and expand or abbreviate lineages, in the process of creating the tree. Recent modifications to taxonomic classification are also highlighted, including an explanation and cited sources supporting the change. An example is the recent reorganization of the mosses (Musci), offering a more accurate reflection of the current understanding of moss phylogeny.
The Tip of the Day addresses some of the finer points of the Taxonomy database and how it is used in other NCBI services. For example, one tip explains why scientific names are sometimes followed by names or abbreviations, as in “Homo sapiens L.” The FAQ section also continues to be a useful source of factual information about the Taxonomy database service. —MR
