[Piggy] MaxEntScan::score5ss for fugu 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

Reference: Yeo G and Burge C.B., Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals, RECOMB 2003

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

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
cagGTAAGT
> dummy2
gagGTAAGT
> dummy3
taaATAAGT
...

Score Fugu 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 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.