Patterns to search for
Enter your search pattern(s) into the text box. Patterns you wish to search for must only contain IUPAC letters.

Pattern collection
Select the database you want to screen. Currently there are three pattern collections that can be screened. PLACE is a plant specific cis-element collection, Jaspar is a high quality cis-element collection that mostly contains cis-elements from vertebrates and Transfac 4.0 (public). Both Jaspar and Tranfac cis-element collections consist only the matrix consensus sequences of the corresponding databases whereas Place collection contains the listed single cis-elements. Choosing "all" screens all these three databases described above.

Similarity score
Similarity score is the precentage value of the number of matching nucleotides between the query pattern (submitted patterns) and the subject pattern (patterns in the database). Only those subject patterns that contain a higher portion of matching nucleotides are reported. The portion is reported in respect of the query pattern and in respect of the subject pattern and the value that is higher is used. For example, the query pattern TTGAC and the subject patterns TTTGACT contains 5 matching nucleotides and thus the score between these two patterns would be 1.00 (5/5) and 0.71 (5/7).

Matching pattern's length
Matching pattern's length is the precentage value of the additional nucleotides between the query pattern (submitted patterns) and the subject pattern (patterns in the database). Only those subject patterns that contain +/- query length * Matching pattern's length nucleotides are analyzed. For example, if the query pattern is TTGAC (length is 5) and Matching pattern's length is 0.20, only patterns which length is between 4 and 6 nucleotides are analyzed.

Penaltize wildcards
When calculating the number of matching nucleotide between the query pattern (submitted patterns) and the subject pattern (patterns in the database), degenerated nucleotides (M, R, W, S, Y, K, V, H, D and N in IUPAC) can be considered either to be absolute or partial matches. If wildcards are penaltiezed (partial match) then N corresponds to 1/4, V, H, D and B corresponds to 1/3 and M, R, W, S, Y and K corresponds to 1/2. For example, the query pattern TTNAC and the subject pattern TTTGACT contains 5 matching nucleotides when wildcards are not penaltiezed and 4.25 matching nucleotides when wildcards are penaltazied.



This tool was developed by Matti Kankainen, University of Helsinki
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