rulai.cshl.orgESEfinder 3.0 - RNA Splicing Enhancer Prediction Tool

last update: 02/27/2007 // Search | background | matrices & thresholds | input & output | caveats Go to ESEfinder2.0 Matrix information Please choose a matrix library: SRProteins SpliceSites hnRNP 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 2. Output format: To a TEXT file ( Output perspective: gene, motif) To a HTML 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: techtran@cshl.edu, phone: 516-367-6885, https://www.cshl.edu/partner-with-us/technology-transfer/ Krainer Lab and Zhang Lab , Cold Spring Harbor Laboratory , all rights reserved Questions/suggestions email: Jinhua Wang...