I am trying to use the software MaxEntScan (http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html)recently. I am kind of confused about its manual. I tried to contact the author, but it seems the email address is no longer available. So I'd like to post the question here to see if anyone has used it before.
On the web page, in order to use the software to score 5' splice sites, the input should be:
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
I am confused here. The UTR 5' is at the beginning of an exon. Should the input sequence be [6 bases in intron] [3 bases in exon]?