RBFTSS is a jar excutable file coded by java enviroment
The classified is a Generalized Radial Basis Function Nueral Network 

Requirement:
java runtime environment version 6 or higher needs to be installed and configured (http://java.sun.com/javase/downloads/index.jsp)
compatability or lower versions of java was not tested



Input File
Input file containing sequences have to be in fasta format

EX:
>NM_000639
AGGATGGGGCAGGGGGGCAGTACACTGAGGGGAGGGTTGAATGATAGTAAT.......
>NM_000815
TGTCTTCGTGTTTGCCGCCCTGGTGGAGTACGCCTTTGCTCATTTCAACGC.......



Specifications
RBFTSS reads sequences in the directoin 5' to 3' only (Forward Strand Only) . Sequences from the negative strand have to be reversed (preprocessed)

RBFTSS gives a cofidence scores at every point of the current sequence only (without considering the reverse complement).

Any character in the sequence that is not any of (A,T,C,G,a,t,c or g) will be randomly substituted.


Output
The resultes will be written to a file in the same directory as the input file as (inputFileName.output)
The cofidence score of the neural network (not probability) will be given at every point (depending on the step size)
It is up to the user how to post process those scores to detect TSS


the output will be formated as
>seq Header
position	confidence score

>NM_000639
600	0.07429609
607	0.06858322
614	0.051372394
.
.

>NM_000815
600	0.103280425
607	0.11563973
.
.


More Details
The original paper is available at:
Online Material is available at:


Contact:
rami mahdi: ramimahdi@yahoo.com