Citation Guidelines for BLAST Software

BLAST (Basic Local Alignment Search Tool) underpins a huge amount of biological research. Just like any other tool or resource, it’s important to cite BLAST and its related software and data sources in your publications.

Do also remember to indicate the version of any software you used, as well as the versions of the datasets you used. The results you obtain with the latest version may be different from those obtained with an older version.

For example, the top of a SequenceServer BLAST report precisely indicate versions:

Citing BLAST

BLAST has evolved through dozens of publications over the years, culminating in the BLAST+ algorithm. While there are many important papers, if you’re using command-line BLAST or the NCBI website, it’s most important to cite current BLAST+ suite:

They have been most recently maintaining and improving the BLAST algorithm, including to ensure that it continues to perform on ever-growing datasets.

Citing Data Sources

If you didn’t generate it yourself as part of your paper, it’s also crucial to cite the your data sources. Here are examples of how to cite common data sources:

Citing SequenceServer

Many use SequenceServer’s graphical interface to run NCBI BLAST searches on custom datasets, or just to get results faster. To cite SequenceServer, use the following reference:

Why cite tools or data sources?

You may wonder why it’s necessary to cite tools and data sources. After all, they’re just resources, and aren’t biological knowledge. The truth is that tools and data sources are just as important as the research itself. Reasons for citing data sources and tools include:

Some historical BLAST references

BLAST has been around for a while - and it has overall been cited more than 100,000 times! You may see some publications also cite older papers. Here are some of the most important ones:

One of the foundational papers for BLAST, where the basic method and its utility in sequence comparison were first introduced:

A paper introducing significant improvements to BLAST, such as Gapped BLAST and PSI-BLAST, enhancing the tool’s accuracy and speed:

A paper discussing how sequence alignments should be scored - a crucial for the BLAST algorithm:

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