Fast.genomics comparative genome browser: 2023 release

This is an archive of the 2023 release of http://fast.genomics.lbl.gov, a fast comparative genome browser for diverse bacteria and archaea.fast_code_Aug2023.tar.gz contains the source code, which is also available at github. See SETUP for installation instructions and lib/neighbor.sql for the database schema.Some of the code depends on Perl libraries from the PaperBLAST code base. These are archived in PaperBLAST_lib.tar.gz and should be exploded into ../PaperBLAST/ to create the ../PaperBLAST/lib directory. They are also available from github.fast_main_May2023.tar.gz contains the main database, with one representative genome for each of 6,377 genera. neighbor.db is the SQLite3 database and neighbor.faa.gz has the protein sequences. Put these files in the data/ directory. You can build the mmseqs database with:gunzip data/neighbor.faa.gzmmseqs createdb data/neighbor.faa data/mmseqsdb --dbtype 1mmseqs createindex data/mmseqsdb /tmp -k 6The sub-databases, with additional genomes for each taxonomic order, can be downloaded here or here. The tarball contains a directory for each sub-database; these subdirectories should go in the data/ directory. After installing the main database, you can build the clustered BLAST+ database for each sub-database's cluster with:for sub in `sqlite3 data/neighbor.db 'select prefix FROM SubDb;'`;do gunzip data/$sub/cluster.faa.gzmakeblastdb -in data/$sub/cluster.faa -dbtype prot -out data/$sub/cluster.faa.plusdbdoneOr, to download the the sub-database for a specific order, visit the fast.genomics web site, search for that order, switch to the sub-database, and see downloads section at the bottom of the main page.