Analysis is done using the SIGSCAN Version 4.05 suite of programs developed by Dr. Dan Prestridge. Information on SIGSCAN is maintained at the Advanced Biosciences Computing Center, University of Minnesota. The IMD database is maintained by Dr. Qing Chen at University of Colorado.
If you use IMD Search program in published research, please cite:
SIGNAL SCAN is offered to you as is, and so are its results, with no promises. A signal, defined here, is any short DNA sequence that may have known significance. What SIGNAL SCAN does is find homologies of published signal sequences in your sequence, most of these transcriptional elements. It cannot, at this time, predict if what it does find, has any meaning. The interpretation of those results are up to you. Most signal elements found probably will not have any meaning, as the elements are in the wrong milieu, wrong cell type, or wrong organism. Consequently, there will be many more erroneous signals found by SIGNAL SCAN than significant ones.
Matrix-search is a program developed to facilitate the analysis of DNA sequences for known transcription factor binding sites. It scores input sequences against matrices of transcription factor binding sites using information theory (Chen, Q.K., Hertz, J.Z. and Stormo, G.D. (1995) MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comp. Appl. Biosciences 11:563-566.) The starting position of patterns with scores above the cutoffs of each matrix are indicated.
In order to reduce false positives, the cutoff scores are determined stringently such that a single base mismatch from the consensus pattern, if not previously demonstrated in our databases, will be deemed by the program as not-matching the consensus pattern. However, more than one mismatch might be allowed if they are documented in the database.
The Match Ratio listed in the output file represents the ratios of the information score of a sequence alignment to an alignment with the maximum score. The higher the P-value of an alignment, the closer it resembles a perfect match.
To visualize the composition of the matrix for a transcription factor, and to get the citation of a journal article about it, please use the Viewing a matrix option in the matrix-search menu.
In the case of overlapping sites for the same factor, only the one with the highest information score is selected.
This program is based on the information theory developed by Dr. Gary Stormo.
Comments and suggestions on the program or additions to the database are welcome. Please contact: Dr. Qing Chen at chenq@beagle.colorado.edu
Return to Signal Scan IMD Search Analysis