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Volumn 9, Issue 8, 2014, Pages

GHOSTX: An improved sequence homology search algorithm using a query suffix array and a database suffix array

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; PROTEIN DATABASE; SEARCH ENGINE; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; ALGORITHM; GENETIC DATABASE; PROCEDURES; SEQUENCE ALIGNMENT;

EID: 84905455179     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0103833     Document Type: Article
Times cited : (74)

References (15)
  • 2
    • 33845874101 scopus 로고    scopus 로고
    • An obesity-associated gut microbiome with increased capacity for energy harvest
    • Available: Accessed 1 November 2012
    • Turnbaugh PJ, Ley RE, Mahowald M a, Magrini V, Mardis ER, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031. Available: http://www.ncbi.nlm.nih.gov/pubmed/17183312. Accessed 1 November 2012.
    • (2006) Nature , vol.444 , pp. 1027-1031
    • Turnbaugh, P.J.1    Ley, R.E.2    Mahowald, M.A.3    Magrini, V.4    Mardis, E.R.5
  • 3
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Available: Accessed 24 May 2013
    • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410. Available: http://linkinghub.elsevier.com/retrieve/pii/S0022283605803602. Accessed 24 May 2013.
    • (1990) Journal of Molecular Biology , vol.215 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3    Myers, E.W.4    Lipman, D.J.5
  • 4
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Available: Accessed 19 February 2014
    • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402. Available: http://www. pubmedcentral.nih.gov/articlerender.fcgi?artid=146917&tool= pmcentrez&rendertype=abstract. Accessed 19 February 2014.
    • (1997) Nucleic Acids Research , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 5
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-Like Alignment Tool
    • doi:10.1101/gr.229202
    • Kent WJ (2002) BLAT - The BLAST-Like Alignment Tool. Genome Research 12: 656-664. doi:10.1101/gr.229202.
    • (2002) Genome Research , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 6
    • 79955877212 scopus 로고    scopus 로고
    • RAPSearch: A fast protein similarity search tool for short reads
    • Available: Accessed 7 September 2011
    • Ye Y, Choi J-H, Tang H (2011) RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics 12: 159. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3113943&tool= pmcentrez&rendertype=abstract. Accessed 7 September 2011.
    • (2011) BMC Bioinformatics , vol.12 , pp. 159
    • Ye, Y.1    Choi, J.-H.2    Tang, H.3
  • 7
    • 84855167751 scopus 로고    scopus 로고
    • RAPSearch2: A fast and memory-efficient protein similarity search tool for next-generation sequencing data
    • Available: Accessed 25 May 2013
    • Zhao Y, Tang H, Ye Y (2012) RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 28: 125-126. Available: http://bioinformatics.oxfordjournals.org/ content/28/1/125. Accessed 25 May 2013.
    • (2012) Bioinformatics , vol.28 , pp. 125-126
    • Zhao, Y.1    Tang, H.2    Ye, Y.3
  • 8
    • 85028161017 scopus 로고
    • Suffix arrays: A new method for on-line string searches
    • Society for Industrial and Applied Mathematics. Available: Accessed 2010 November 8
    • Manber U, Myers G (1990) Suffix arrays: a new method for on-line string searches. Proceedings of the first annual ACM-SIAM symposium on Discrete algorithms. Society for Industrial and Applied Mathematics. 319-327. Available: http://portal.acm.org/citation.cfm?id=320176.320218&coll=portal&dl= ACM&type=series&idx=SERIES422&part=series&WantType= Proceedings&title=Symposium. Accessed 2010 November 8.
    • (1990) Proceedings of the First Annual ACM-SIAM Symposium on Discrete Algorithms , pp. 319-327
    • Manber, U.1    Myers, G.2
  • 9
    • 78651415181 scopus 로고    scopus 로고
    • GPU-BLAST: Using graphics processors to accelerate protein sequence alignment
    • Available: Accessed 013 November 8
    • Vouzis PD, Sahinidis NV (2011) GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics 27: 182-188. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3018811&tool= pmcentrez&rendertype=abstract. Accessed 013 November 8.
    • (2011) Bioinformatics , vol.27 , pp. 182-188
    • Vouzis, P.D.1    Sahinidis, N.V.2
  • 10
    • 74549131031 scopus 로고    scopus 로고
    • Inexact Local Alignment Search over Suffix Arrays
    • Available: Accessed 2013 July 12
    • Ghodsi M, Pop M (2009) Inexact Local Alignment Search over Suffix Arrays. Proceedings IEEE International Conference on Bioinformatics and Biomedicine 2009: 83-97. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=3029072&tool=pmcentrez&rendertype=abstract. Accessed 2013 July 12.
    • (2009) Proceedings IEEE International Conference on Bioinformatics and Biomedicine 2009 , pp. 83-97
    • Ghodsi, M.1    Pop, M.2
  • 11
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Available: Accessed 2013 May 27
    • Kanehisa M (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 28: 27-30. Available: http://www.nar.oupjournals.org/cgi/doi/10. 1093/nar/27.1.29. Accessed 2013 May 27.
    • (2000) Nucleic Acids Research , vol.28 , pp. 27-30
    • Kanehisa, M.1
  • 12
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Available: Accessed 2013 May 22
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research 40: D109-14. Available: http://www.pubmedcentral.nih.gov/ articlerender.fcgi?artid=3245020&tool=pmcentrez&rendertype=abstract. Accessed 2013 May 22.
    • (2012) Nucleic Acids Research , vol.40
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 13
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • The Human Microbiome Project Consortium Available: Accessed 2014 January 20
    • The Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3564958&tool= pmcentrez&rendertype=abstract. Accessed 2014 January 20.
    • (2012) Nature , vol.486 , pp. 207-214
  • 14
    • 0025950944 scopus 로고
    • Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
    • doi:10.1016/0888-7543(91)90071-L
    • Pearson WR (1991) Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11: 635-650. doi:10.1016/0888-7543(91)90071-L.
    • (1991) Genomics , vol.11 , pp. 635-650
    • Pearson, W.R.1
  • 15
    • 27144489108 scopus 로고    scopus 로고
    • Protein database searches using compositionally adjusted substitution matrices
    • Available: Accessed 2011 August 3
    • Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, et al. (2005) Protein database searches using compositionally adjusted substitution matrices. The FEBS journal 272: 5101-5109. Available: http://www.pubmedcentral.nih.gov/ articlerender.fcgi?artid=1343503&tool=pmcentrez&rendertype=abstract. Accessed 2011 August 3.
    • (2005) The FEBS Journal , vol.272 , pp. 5101-5109
    • Altschul, S.F.1    Wootton, J.C.2    Gertz, E.M.3    Agarwala, R.4    Morgulis, A.5


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