[Piggy] MaxEntScan::score5ss for human 5' splice sites

Burge Lab

MaxEntScan::score5ss scores 9 mers using different 5'ss models

To score 3' splice sites go to MaxEntScan::score3ss

To build your own MaxEntScan models as described in the paper (below) refer to MaxEntScan::build
MaxEntScan is based on the approach for modeling the sequences of short sequence motifs such as those involved in RNA splicing which simultaneously accounts for non-adjacent as well as adjacent dependencies between positions. This method is based on the 'Maximum Entropy Principle' and generalizes most previous probabilistic models of sequence motifs such as weight matrix models and inhomogeneous Markov models.

References: Yeo G and Burge C.B., Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals, RECOMB 2003 (Journal Comp. Bio in press)

Our models have been used in a successful collaboration which involves predicting splicing mutations: Eng L, Coutinho G, Nahas S, Yeo G, Tanouye R, Babaei M, Dork T, Burge C, Gatti RA. Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths. Hum Mutat. 2004 Jan; 23(1):67-76

For questions and comments please email Gene at geneyeo@mit.edu.

To download splice site datasets: Download splice site datasets
To download simple perl scripts to run our algorithm on your own:
Download perl wrappers

How to use MaxEntScan::score5ss

Each sequence must be 9 bases long. [3 bases in exon][6 bases in intron]
Input sequences as a FastA file with one sequence per line (no linebreaks). Non-ACGT sequences will not be processed.

Example Fasta File
> dummy1
> dummy2
> dummy3

Score Human 5' splice sites

Upload 9-mer SEQUENCES filename:

Or you can enter your fasta format 9-mer sequences:

Choice of Scoring Models

Use Maximum Entropy Model to score: (Check if YES,default is NO)
Use Maximum Dependence Decomposition Model to score: (Check if YES,default is NO)
Use First-order Markov Model to score: (Check if YES,default is NO)
Use Weight Matrix Model to score: (Check if YES,default is NO)

This algorithm was developed by Gene Yeo
geneyeo@mit.edu and Christopher Burge cburge@mit.edu. This material is based upon work supported by the National Science Foundation (NSF) under Grant No. 0218506. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the NSF.