December 2023 release of the databases for PaperBLAST, Curated BLAST for Genomes, and SitesBLAST

This includes the December 2023 release of three related tools: PaperBLAST, Curated BLAST for Genomes, and SitesBLAST. PaperBLAST links protein sequences to papers about them and to curated annotations. Curated BLAST for Genomes uses the characterized subset of PaperBLAST's database to find candidates with a function of interest within a genome. SitesBLAST links protein sequences to functional sites, such as catalytic residues or substrate-binding residues.Most of the files are gzipped:litsearch.db -- the sqlite3 database for PaperBLAST and SitesBLAST. Also see the schema.litsearch.faa -- sequences for all of the proteins mentioned in the Gene or CuratedGene tables, in fasta formatuniq.faa -- unique sequences from litsearch.faa, in fasta format. (Also see the SeqToDuplicate table.)stats -- some statistics on the PaperBLAST databasecurated.faa -- the curated subset of PaperBLAST's database, in fasta formathassites.faa -- sequences for all the proteins mentioned in the HasSites table, in fasta format.To run the tools from these downloaded databases, you need to gunzip the files and format the BLAST databases. For more information see here.References:PaperBLAST: Text Mining Papers for Information about Homologs (mSystems, 2017)Curated BLAST for Genomes (mSystems, 2020)Interactive Analysis of Functional Residues in Protein Families (mSystems, 2022)