Does anyone know how to cite NCBI wwwblast in a manuscript ? I hope someone used it before in a publication. I haven't seen any paper on it so I was wondering whether I should use just the web address to cite it? http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/wwwblast/.
For the on-line BLAST web interface provided by NCBI, and if the context allows it, you could cite the "The BLAST Sequence Analysis Tool" chapter in the NCBI Handbook:
Madden T. The BLAST Sequence Analysis Tool. 2002 Oct 9 [Updated 2003 Aug 13]. In: McEntyre J, Ostell J, editors. The NCBI Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-. Chapter 16. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21097/
If this is not an option, there are a number of other options, including:
Note: the paper mentioned by David Westergaard: Wheeler, D.L. et al. (2007) "Database resources of the National Center for Biotechnology Information", is the 2007 version of the 2013 paper mentioned above. NCBI publish a version of this paper every year in the Database issue of Nucleic Acids Research, these papers are a go to location for figuring out the current references for resources provided by the NCBI.
For the command-line version of NCBI BLAST, and for details of the BLAST method, you would cite:
For the legacy wwwBLAST distribution, which was a locally installable implementation of the NCBI BLAST web interface (see ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST), you will likely need to cite a mixture of these papers. That said the only paper I can find which talks about wwwBLAST is Wiezer, A. and Merkl, R. (2003) "secureBLAST", and it cites the 1990 BLAST paper (and probably should have cited the 1997 one, since that describes NCBI BLAST version 2.x and as far as I am aware the web interface was not available for NCBI BLAST version 1.x).
The exact paper(s) you need to cite will depend on which aspects of NCBI BLAST you are writing about, if you are just mentioning the service or the program then the first paper in each group above would most likely apply. If instead you are referring to specific aspects of the web interface or the BLAST method, then you will need to find the paper(s) associated with those aspects.
Note: some features of NCBI BLAST, such as compositional statistics and low complexity sequence filtering have their own references, which can be found in the BLAST documentation.
If you are using an alternative implementation of the BLAST algorithm, then while some of the above may apply you will also want to look for papers specific to the implementation. For example:
I don't think there is any paper associated with the actual server. And it's quite uncommon to cite BLAST nowadays. Since it's such a common tool, it would be like citing a pipette. I would think it OK to just mention the ressource along with version and provide a URL. I don't think it would hurt either to cite the NCBI resources paper.
Mind you, I am not affiliated with the NCBI. If you want a correct answer, it would probably be best to write the NCBI BLAST helpdesk.
Most people just cite the Altschul et al BLAST paper itself (although as pointed out it is so common that sometimes it goes uncited)
I use command line BLAST and it is the latest version of BLAST. So I believe the citation given in it can also be given for the online blast. Here is the citation:
Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14
This is the orginal MegaBLAST paper, and has been superceded by:
Morgulis, A. et al. (2008) "Database indexing for production MegaBLAST searches"
Now that MegaBLAST has been integrated into NCBI BLAST+ the most appropriate citation would really be that for BLAST+:
Camacho C. et al. (2009) "BLAST+: architecture and applications"
Assuming that you are using the NCBI BLAST+ implementation.
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Ah, good point! Time to update my NCBI reference.