Phyloscan Explained

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.

External links

• Phyloscan homepage at Brown University

Notes and References

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