Phyloscan

Phyloscan

Phyloscan

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Phyloscan[1][2] is a web service for DNA sequence analysis that is free and open to all users (without login requirement). For locating matches to a user-specified sequence motif for a regulatory binding site, Phyloscan provides a statistically sensitive scan of user-supplied mixed aligned and unaligned DNA sequence data. Phyloscan's strength is that it brings together

  • the Staden method[3] for computing statistical significance,
  • the "phylogenetic motif model" scanning functionality of the MONKEY software[4] that models evolutionary relationships among aligned sequences,
  • the use of the Bailey & Gribskov method[5] for combining statistics across non-aligned sequence data, and
  • the Neuwald & Green technique[6] for combining statistics across multiple binding sites found within a single gene promoter region.
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References

  1. [1]
    Palumbo, MJ; Newberg, LA (July 1, 2010). "Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data". Nucleic Acids Research. 38 (Web server issue): W268–W274. doi:10.1093/nar/gkq330. PMC 2896078. PMID 20435683.
  2. [2]
    Carmack, CS; McCue, LA; Newberg, LA; Lawrence, CE (January 23, 2007). "PhyloScan: identification of transcription factor binding sites using cross-species evidence". Algorithms for Molecular Biology. 2 (1): article 1. doi:10.1186/1748-7188-2-1. PMC 1794230. PMID 17244358.
  3. [3]
    Staden, R (April 1989). "Methods for calculating the probabilities of finding patterns in sequences". Computer Applications in the Biosciences. 5 (2): 89–96. doi:10.1093/bioinformatics/5.2.89. PMID 2720468.
  4. [4]
    Moses, AM; Chiang, DY; Pollard, DA; Iyer, VN; Eisen, MB (November 30, 2004). "MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model". Genome Biology. 5 (12): R98. doi:10.1186/gb-2004-5-12-r98. PMC 545801. PMID 15575972.
  5. [5]
    Bailey, TL; Gribskov, M (Summer 1998). "Methods and statistics for combining motif match scores". Journal of Computational Biology. 5 (2): 211–221. doi:10.1089/cmb.1998.5.211. PMID 9672829.
  6. [6]
    Neuwald, AF; Green, P (June 24, 1994). "Detecting patterns in protein sequences". Journal of Molecular Biology. 239 (5): 698–712. doi:10.1006/jmbi.1994.1407. PMID 8014990.
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