We’ve made some recent enhancements to the BLAST+ applications that allow you to:
- Limit your search by taxonomy using information built into the BLAST databases
- Search sequences by accession faster
- Use blastdbcmd to retrieve sequences by taxonomy from a BLAST database
The new version of the BLAST databases (version 5, release notes) supports the items listed above. You can access the new executables on FTP. Sample version 5 databases are also available.
Note: This is an alpha release to allow users to test and comment on new features.
Please send problem reports and feedback to email@example.com or write to the Help Desk.
NCBI is now producing a new set of taxonomy files that include the taxonomic lineage of taxa, information on type strains and material, and host information. These files are particularly helpful for people maintaining local installations of NCBI data.
You can download the new archive (new_taxdump.tar.gz) from the taxonomy directory on the FTP site (ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/). The new files are typematerial.dmp, typeoftype.dmp, rankedlineage.dmp, fullnamelineage.dmp,
taxidlineage.dmp, and host.dmp. Please see the readme file for details of the file contents.
The original taxonomy file archive without the new content will remain available under its original name, taxdump.tar.gz. The section below shows the entries for the monkey species Cercopithecus lomamiensis from the new ranked lineage and type material files. Continue reading “New taxonomy files available with lineage, type, and host information”