xmlBLASTparser

xmlBLASTparser V1.1 — A PHP BASED NCBI BLAST XML OUTPUT PARSER

Ashok Kumar T., B. Rajagopal

Abstract


xmlBLASTparser is a lightweight PHP library for parsing an XML formatted output of NCBI BLAST sequence alignment and rendering into attractive web page. The biological database accession numbers present in each sequence alignment hit have properly hyperlinked to the original source. Moreover, hit ids in the description summary is anchor hyperlinked to the corresponding sequence alignment section. The xmlBLASTparser library can be easily embedded or integrated in a web page at server-side through standalone NCBI BLAST software or RESTful web service of NCBI BLAST. The output of xmlBLASTparser has the same flavour of the online NCBI BLAST. xmlBLASTparser is freely available under terms of GNU General Public License version 3 (GPLv3), at https://github.com/AshokHub/xmlBLASTparser.

Keywords


xmlBLASTparser; PHP library; Sequence alignment; XML output parser; NCBI BLAST

Full Text:

PDF

References


S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, "Basic local alignment search tool," J. Mol. Biol., vol. 215, no. 3, pp. 403–410, Oct. 1990, doi:10.1016/S0022-2836(05)80360-2.

S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs," Nucleic Acids Res., vol. 25, no. 17, pp. 3389–3402, Sep. 1997.

C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer, and T. L. Madden, "BLAST+: architecture and applications," BMC Bioinformatics, vol. 10, no. 1, p. 421, 2009, doi:10.1186/1471-2105-10-421.

NCBI BLAST - https://blast.ncbi.nlm.nih.gov/Blast.cgi

T. Madden, "The BLAST Sequence Analysis Tool," 15 Mar. 2013, In: The NCBI Handbook, 2nd ed., Bethesda (MD): National Center for Biotechnology Information (US), 2013. Available from:

https://www.ncbi.nlm.nih.gov/books/NBK153387/

T. Ashok Kumar and B. Rajagopal, “BLASTphp: a PHP wrapper for NCBI BLAST API,” Int. J. Comp. Bio., vol. 6, no. 1, pp. 31-33, Jul. 2017.

Extensible Markup Language (XML), In: W3C, Retrieved from https://www.w3.org/XML/, Accessed 25 Aug. 2017.

NCBI BLAST Output DTD, In: NCBI, Retrieved from https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd, Accessed 25 Aug. 2017.




DOI: https://doi.org/10.26483/ijarcs.v8i8.4648

Refbacks





Copyright (c) 2017 International Journal of Advanced Research in Computer Science