findCNS

finding conserved regions in grass genomes

Compile the program

g++ -o findCNS findCNS.cpp

Run the program

./findCNS -file fasta_file -mem minimum_CNS_length -gff gff_Filename -out prefix_output_file > out.txt

Example: ./findCNS -file test.fasta -mem 8 -gff gffnames.txt -out TEST > out.txt

Outputs

1. TEST_CNS_8.csv (contains CNS information)
2. TEST_MEM_1_8.csv (contains all MEMs)
3. TEST_MEM_2_8.csv (contains all MEMs without serial number)
4. TEST_LPMEM_8_csv (contains all CNSs without actual chromosome location )
5. TEST_MEM_8.html (used for browser visualization )
6. TEST_LPMEM_8.html (used for browser visualization)
7. out.txt (contains all console outputs and error logs)

The first file contains the CNS information. The other files are used for visualization.

Visualization

Two ways to visualiza the output

1. Using XDAT: Run the collowing command on command line

   java -jar xdat.jar

   It will open an window where the TEST_MEM_2_8.csv and TEST_LPMEM_8_csv files can be uploaded (data) to see the visualizations (chart->parallel coordinate set). Don't forget to change the settings (import settings) to accept comma separated files.

2. Using browser (firefox) Run the following commands:

firefox TEST_MEM_8.html

firefox TEST_LPMEM_8.html

3. Gobe Visualization will be added