Phyloscan
Encyclopedia
Phyloscan 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
Sequence analysis
In bioinformatics, the term sequence analysis refers to the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alignment, searches against biological...
that is free and open to all users (without login requirement). For locating matches to a user-specified sequence motif
Sequence motif
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance...
for a regulatory binding site
DNA binding site
DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that they are part of a DNA sequence and they are bound by DNA-binding proteins...
, Phyloscan provides a statistically sensitive
Sensitivity and specificity
Sensitivity and specificity are statistical measures of the performance of a binary classification test, also known in statistics as classification function. Sensitivity measures the proportion of actual positives which are correctly identified as such Sensitivity and specificity are statistical...
scan of user-supplied mixed aligned
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
and unaligned DNA sequence data. Phyloscan's strength is that it brings together
- the Staden method for computing statistical significanceStatistical significanceIn statistics, a result is called statistically significant if it is unlikely to have occurred by chance. The phrase test of significance was coined by Ronald Fisher....
, - the "phylogenetic motif model" scanning functionality of the MONKEY software that models evolutionary relationships among aligned sequences,
- the use of the Bailey & Gribskov method for combining statistics across non-aligned sequence data, and
- the Neuwald & Green technique for combining statistics across multiple binding sites found within a single gene promoter region.