Binding Matrix Calculator

This site provides an electronic service for calculating the binding matrix, a novel method for detecting binding sites described in a manuscript which is currently under review for the Journal of Bioinformatics and Computational Biology.

Instructions

Please type or paste a set of known binding words for one transcription factor into the form below. The set of binding words must be given as a gapless multiple alignment in FASTA format. You may choose to have the matrix rendered in the standard normal form (which typically contains negative values) or in the profile matrix form (in which values in one row add up to 1).

As a result, you will receive the binding matrix, computed from your input sequences. Additionally, the profile matrix is also computed. Both are output in a format which is primarily intended for viewing, but should be reasonably easily convertible into machine readable formats.

Alternatively, a matrix in a format suitable for use with the profit program of the EMBOSS package, version 2.5.1, can be obtained by checking the corresponding option in the form below. A matrix generated with this option can be saved into a file (e.g. by using the "Save Page As..." menu item of your browser), and then used with the profit program. Technically, generating a profit-formatted matrix involves

• computing the binding matrix in the profile matrix form
• multiplying matrix components by 1000 and rendering them as integers
• filling in columns corresponding to letters other than a, c, g and t with zeroes
• rendering the threshold as a percentage of the maximal score.

For an experience of the effective difference between the binding matrix and the profile matrix, use the prophecy program from the EMBOSS package to compute a profile matrix from your binding words and use this profile matrix and the binding matrix obtained from this server to scan sequences that you are familiar with.

Suggestions for improvements of this service are welcome.