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)本数据集收录2023年12月发布的三款关联工具：PaperBLAST、基因组专用精选BLAST（Curated BLAST for Genomes）及SitesBLAST。其中，PaperBLAST可实现蛋白质序列与其相关研究论文及精选注释的关联；基因组专用精选BLAST（Curated BLAST for Genomes）依托PaperBLAST数据库的已表征子集，可在基因组范围内筛选出携带目标功能的候选序列；SitesBLAST则可将蛋白质序列与功能位点（如催化残基、底物结合残基）进行关联。 多数文件采用gzip压缩格式，具体如下： - litsearch.db：供PaperBLAST与SitesBLAST使用的SQLite3数据库，亦可参考其数据架构（schema）。 - litsearch.faa：以FASTA格式存储的Gene表或CuratedGene表中提及的全部蛋白质序列。 - uniq.faa：以FASTA格式存储的litsearch.faa去重序列（亦可参考SeqToDuplicate表）。 - stats：PaperBLAST数据库的相关统计信息。 - curated.faa：以FASTA格式存储的PaperBLAST数据库精选子集序列。 - hassites.faa：以FASTA格式存储的HasSites表中提及的全部蛋白质序列。 若需基于本次下载的数据库运行上述工具，请先对压缩文件进行解压缩，并完成BLAST数据库的格式构建。更多详情可查看此处。 参考文献： 1. PaperBLAST：《基于文献文本挖掘获取同源基因信息》（mSystems，2017年） 2. 基因组专用精选BLAST（Curated BLAST for Genomes）（mSystems，2020年） 3. 《蛋白质家族功能残基的交互式分析》（mSystems，2022年）