BLASTphp: a PHP wrapper for NCBI BLAST API

T. Ashok Kumar

Abstract


NCBI BLAST is a most popular bioinformatics framework for finding local similarity between two or more biological sequences. It provides integrative access to various biological databases through web user interface, command-line user interface, and application programming interface. BLASTphp is a lightweight PHP library that wrap’s NCBI BLAST’s RESTful API into a custom graphical user interface BLAST. The BLASTphp program remotely executes the NCBI BLAST through the HTTP/HTTPS interface and elicits the response in HTML, XML, XML2, JSON2, Text, or Tabular (plain) format. However, it can be easily connected to a webserver and integrated with any SQL database which contain the biological sequences. BLASTphp is freely available under GNU General Public License version 3 (GPLv3), at https://github.com/AshokHub/BLASTphp.

Keywords


PHP BLAST; BLAST RESTful API; Remote BLAST; Sequence Alignment; BLAST PHP Library

Full Text:

PDF

References


Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990 Oct;215(3):403–10. Cited in PubMed; PMID 2231712.

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 1997 Sep 1;25(17):3389–402. Cited in PubMed; PMID 9254694.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10(1):421. Cited in PubMed; PMID 20003500.

Tatusova TA, Madden TL. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiology Letters. 1999 May 15;174(2):247–50. Cited in PubMed; PMID 10339815.

Madden T. The BLAST Sequence Analysis Tool. 2013 Mar 15. In: The NCBI Handbook [Internet]. 2nd edition. Bethesda (MD): National Center for Biotechnology Information (US); 2013-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK153387/

BLAST. In: Wikipedia [Internet]. 2017 Jan 06. Available from: https://en.wikipedia.org/wiki/BLAST

Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Research. 2002 Oct;12(10):1611–8. Cited in PubMed; PMID 12368254.

Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 1;25(11):1422–3. Cited in PubMed; PMID 19304878.

Holland RCG, Down TA, Pocock M, Prlić A, Huen D, James K, et al. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008 Sep 15;24(18):2096–7. Cited in PubMed; PMID 18689808.

Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T. BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics. 2010 Oct 15;26(20):2617–9. Cited in PubMed; PMID 20739307.