使用 Homebrew, Nix 安装 blast

项目链接

• 主页

命令和别名

• blast_formatter
• blastdb_aliastool
• blastdb_convert
• blastdb_path
• blastdbcheck
• blastdbcmd
• blastdbcp
• blastn
• blastp
• blastx
• cleanup-blastdb-volumes.py
• convert2blastmask
• datatool
• deltablast
• dustmasker
• gc_cli
• get_species_taxids.sh
• legacy_blast.pl
• lmdbxx_sample
• makeblastdb
• makeclusterdb
• makembindex
• makeprofiledb
• project_tree_builder
• psiblast
• rpsblast
• rpstblastn
• run_with_lock
• seedtop
• segmasker
• seqdb_demo
• seqdb_perf

项目历史

NCBI's BLAST help references the 1990 Altschul, Gish, Miller, Myers, and Lipman paper that introduced the Basic Local Alignment Search Tool. The same NCBI reference list traces later BLAST-family milestones including gapped BLAST and PSI-BLAST in 1997, MegaBLAST indexing work in 2008, BLAST+ architecture in 2008, DELTA-BLAST in 2012, Magic-BLAST in 2019, and ElasticBLAST in 2023.

The command-line package distributed today is BLAST+, documented by NCBI's BLAST Command Line Applications User Manual. The developer information page identifies BLAST as public-domain software and points developers to the NCBI C++ Toolkit implementation, matching the public GitHub toolkit repository used for source distribution.

采用历史

BLAST became a standard because it joined a fast heuristic alignment algorithm with NCBI's growing public sequence databases. Web BLAST made ad hoc searches accessible, while the command-line applications let labs, sequencing centers, and pipelines run repeatable local searches against custom databases.

Package-manager adoption reflects that role: even when the upstream distribution is from NCBI rather than a typical single-purpose GitHub project, package managers keep `blastn`, `blastp`, `blastx`, `makeblastdb`, `blastdbcmd`, and related executables available as system tools for bioinformatics workflows.

使用方式

Common local workflows build a database with `makeblastdb`, search it with tools such as `blastn` or `blastp`, inspect databases with `blastdbcmd`, and format results with `blast_formatter`. NCBI also documents REST access for programmatic searches against hosted services.

The package contains a family of executables rather than one command. That matters for reproducible science because database construction, masking, protein-vs-nucleotide search modes, profile searches, and output formatting are split into scriptable tools.

为什么软件包爱好者会关心

For package nerds, BLAST is a canonical example of scientific infrastructure as a Unix package: many binaries, public-domain licensing, local database files, environment/config conventions, and a manual that is closer to laboratory protocol than app documentation.

It is also a reminder that the most important command-line tools are not always developer tools. BLAST made local compute a practical front end to public biological databases, so packaging it well directly affected how biology labs automated sequence analysis.

时间线

• 1990: Original BLAST paper published.
• 1997: Gapped BLAST and PSI-BLAST paper published.
• 2008: NCBI BLAST Command Line Applications User Manual citation date and BLAST+ architecture paper appear.
• 2012: DELTA-BLAST paper published.
• 2019: Magic-BLAST paper published.
• 2023: ElasticBLAST cloud-search paper published.

Related projects

• Related projects and descendants include PSI-BLAST, MegaBLAST, DELTA-BLAST, Magic-BLAST, ElasticBLAST, the NCBI C++ Toolkit, FASTA-family sequence search tools, and downstream workflow systems that wrap BLAST searches.

来源

• https://blast.ncbi.nlm.nih.gov/doc/blast-help/developerinfo.html
• https://blast.ncbi.nlm.nih.gov/doc/blast-help/references.html
• https://github.com/ncbi/ncbi-cxx-toolkit-public
• https://www.ncbi.nlm.nih.gov/books/NBK279690