Phyloscan

{{Infobox Software

| name = Phyloscan

| developer = Wadsworth Center, New York State Department of Health

| released = {{release date|2005|03|14}}

| latest release version = 2.2

| latest release date = {{release date|2010|01|28}}

| platform = web service

| language = English

| genre = Bioinformatics tool

| website = http://ccmbweb.ccv.brown.edu/cgi-bin/phyloscanV2.pl

}}

Phyloscan{{cite journal |last1=Palumbo |first1=MJ |last2=Newberg |first2=LA |title=Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data |journal=Nucleic Acids Research |volume=38 |issue=Web server issue |pages=W268–W274 |date=July 1, 2010|doi=10.1093/nar/gkq330 |pmc=2896078 |pmid=20435683}}{{cite journal |last1=Carmack |first1=CS |last2=McCue |first2=LA |last3=Newberg |first3=LA |last4=Lawrence |first4=CE |title=PhyloScan: identification of transcription factor binding sites using cross-species evidence |journal=Algorithms for Molecular Biology |volume=2 |issue=1 |pages=article 1 |date=January 23, 2007|doi=10.1186/1748-7188-2-1 |pmid=17244358 |pmc=1794230 |doi-access=free }} 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{{cite journal |last1=Staden |first1=R |title=Methods for calculating the probabilities of finding patterns in sequences |journal=Computer Applications in the Biosciences |volume=5 |issue=2 |pages=89–96 |date=April 1989 |doi=10.1093/bioinformatics/5.2.89 |pmid=2720468}} for computing statistical significance,
• the "phylogenetic motif model" scanning functionality of the MONKEY software{{cite journal |last1=Moses |first1=AM |last2=Chiang |first2=DY |last3=Pollard |first3=DA |last4=Iyer |first4=VN |last5=Eisen |first5=MB |title=MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model |journal=Genome Biology |volume=5 |issue=12 |pages=R98 |date=November 30, 2004|doi=10.1186/gb-2004-5-12-r98 |pmid=15575972 |pmc=545801 |doi-access=free }} that models evolutionary relationships among aligned sequences,
• the use of the Bailey & Gribskov method{{cite journal |last1=Bailey |first1=TL |last2=Gribskov |first2=M |title=Methods and statistics for combining motif match scores |journal=Journal of Computational Biology |volume=5 |issue=2 |pages=211–221 |date=Summer 1998 |doi=10.1089/cmb.1998.5.211 |pmid=9672829}} for combining statistics across non-aligned sequence data, and
• the Neuwald & Green technique{{cite journal |last1=Neuwald |first1=AF |last2=Green |first2=P |title=Detecting patterns in protein sequences |journal=Journal of Molecular Biology |volume=239 |issue=5 |pages=698–712 |date=June 24, 1994 |doi=10.1006/jmbi.1994.1407 |pmid=8014990}} for combining statistics across multiple binding sites found within a single gene promoter region.