Prof. Dan Mishmar



Welcome to LEMONS:

A Tool for Identifying Splice Junction in

High-Throughput Data without a Reference Genome



1. Download and Installation:

(For LEMONS Graphical User Interface (GUI) skip to step 3)


1.1  Download the LEMONS ZIP archives here: win_32 or win_64. 

      The source code is available here.

1.2  Save the file on your computer, open it (double click) and the “LEMONS” folder will Appear. Copy this folder to the desired location.

1.3  In order for “LEMONS” to operate, “BLAST” should be installed on your computer. If it is not, you can download it from the “NCBI” ftp site here for windows 32 bit or for windows 64 bit. NOTE: If you don’t know which type of windows is installed on your computer, choose the windows 32 bit . To install BLAST  - double click on the downloaded file and follow the instructions. NOTE: Do not change the installation location of the BLAST software! (see Fig 1)


1.4 The LEMONS user manual can be download here.

2. The Data used in the Manuscript: TransCham2(D12).rar

Fig 1:










3.LEMONS Graphical User Interface (GUI)

3.1 Download LEMONS GUI here: win_32 or win_64

3.2 Follow the instructions as in 1.2 and 1.3

3.3 Double click the icon: 




4.LEMONS Database Generator

4.1 The LEMONS Database Generator is an integral part of LEMONS and LEMONS GUI (see 1.1 and 3.1)

4.2 Double click the icon: 














4.3 Follow the instructions outlined in the tutorial here


5.LEMONS on linux:

5.1 LEMONS is available on linux as a python script: here

5.2 You need to have both python and BLAST installed on your system.

5.3 Both need to be in the PATH and you should be able to run them from anywhere.

5.4 LEMONS works in the same manner on linux and on windows command line.

5.5  $ tar -zxvf LEMONS.tar.gz

5.6  $ cd LEMONS

5.7  $ python --in "Example.fasta" 


If you have any questions or requests, please contact us by e-mail: