last update: 02/27/2007

Search | background | matrices & thresholds | input & output | caveats

Go to ESEfinder2.0

Matrix information

Please choose a matrix library:

Choose the matrix and the threshold to be used:

Matrices (select one or more) Threshold
SF2/ASF (SF2/ASF round 3 winner)
SF2/ASF (IgM-BRCA1) (Smith06-HMG-matrix)
SC35 (SC35 round 3 winner)
SRp40 (SRp40 round 3 winner)
SRp55 (SRp55 round 3 winner)

Sequence information

Enter here your input data in FASTA or MULTI-FASTA format (<5000nt, accept both 'T' and 'U' as being equivalent)
(please read important information about search format description)

alternatively, upload a text file:

Output information

Override the thresholds above and use one of the following two options:
Report only the best hit in each sequence (instead of hits above the thresholds)
Report all scores in each sequence (instead of hits above the thresholds)

(Note: if you check both, the program will report the best hit in each sequence.)

Output as a plain text file

please send the results to the following e-mail address:

Citation information

In referring to work done using ESEfinder(c), please cite:

Smith, P. J., Zhang, C., Wang, J. Chew, S. L., Zhang, M. Q. and Krainer, A. R. 2006.
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.
Hum. Mol. Genet. 15(16): 2490-2508.

Cartegni L., Wang J., Zhu Z., Zhang M. Q., Krainer A. R.; 2003.
ESEfinder: a web resource to identify exonic splicing enhancers.
Nucleic Acid Research, 2003, 31(13): 3568-3571.

ESEfinder (2001-2006, Cold Spring Harbor Laboratory) can be used for free by non-profit
institutions for non-commercial purposes.    Commercial users of the program or of
parts of it may obtain a site license and should contact 
Email:,  phone: 516-367-6885,

Krainer Lab and Zhang Lab, Cold Spring Harbor Laboratory, all rights reserved
Questions/suggestions email: Jinhua Wang.