

The Stepgram application is used to detect aberrations in DNA copy number data from aCGH experiments. The application is based on the interval score described in the paper "Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis" (Proceedings of RECOMB 05, and JCB 06),  
Features of the Stepgram application:

 
Aberration calling in Stepgram is based on the Interval Score defined in (Lipson et al, RECOMB 05). This score describes, for each genomic interval I, the deviation of the sum of signals in the interval from the zero baseline:
where x_{i} is the i'th elements in the data vector, and is the noise level of the data, measured as the derivative logratio spread (DLRS) of the signal over the entire genome. The interval I that maximizes the score S(I) is determined using the efficient LookAhead algorithm. If this score passes a given threshold, then I is marked as aberrant, and the procedure is repeated recursively to the left and right of I, and also within I  to search for nested aberrations. The recursion is stopped when no interval with a score surpassing the given threshold is found. 

Stepgram is available as a Win32 executable (version 2.12, tested on Windows XP):


Stepgram output is easily imported to and visualized in external applications, such as Excel, Origin etc:


If you choose to use this application in your research, please cite:


Contact Info  
For additional Information please contact Doron Lipson, CS Department, Technion, Israel. 