Question: 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/.

Answer: 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:

NCBI Resource Coordinators (2013) "Database resources of the National Center for Biotechnology Information"

Boratyn, G.M. et al. (2013) "BLAST: a more efficient report with usability improvements"

Johnson M. et al. (2008) "NCBI BLAST: a better web interface"

Note: the paper mentioned by David: 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:

Camacho C. et al. (2009) "BLAST+: architecture and applications"

Altschul S.F. et al. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs"

Altschul S.F. et al. (1990) "Basic local alignment search tool"

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:

Angermüller, C., Biegert, A. and Söding, J. (2012) "Discriminative modelling of context-specific amino acid substitution probabilities"

Vouzis, P.D. and Sahinidis, N.V. (2010) "GPU-BLAST: using graphics processors to accelerate protein sequence alignment"

Oehmen, C.S. and Baxter, D.J. (2013) "ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems"

Lopez, R. et al. (2003) "WU-Blast2 server at the European Bioinformatics Institute"