CASPER SeqFinder Algorithm

This algorithm searches through an input genomic sequence file (FASTA/FNA) and finds all unique and repeated guide-RNA (gRNA) sequences for a given Cas endonuclease. It outputs two files:

1. CSPR file containing a list of all unique gRNAs
2. SQL DB file containing all repeated gRNAs

Download And Compile Sqlite3

Linux:

1. Open terminal
2. Run the following command: sudo apt-get install sqlite3

Mac and Linux (if you did not use apt-get):

1. Download sqlite3 source code
2. Open terminal
3. CD to sqlite3 source code folder
4. Build using the following command: gcc -c sqlite3.c
   • The build command should generate a .o file that will be used with compiling SeqFinder.
5. Copy the .o file to the SeqFinder source code folder

Windows (Visual Studio 2017):

1. Download sqlite3 source code
2. Open "Developer Command Prompt for VS 2017"
3. CD to sqlite3 source code folder
4. Build the library files by running the following command: lib /DEF:sqlite3.def /OUT:sqlite3.lib /MACHINE:x64

Download and Compile Seq-Finder

Linux (if you used apt-get install sqlite3):

1. Download SeqFinder source code for Linux (in Repository)
2. Open terminal
3. CD to Seq-Finder source code folder
4. Run Command to compile SeqFinder: g++ -std=c++11 *.cpp -pthread -l sqlite3 -o SeqFinder

Mac and Linux (if you manually built sqlite3 .o file, make sure sqlite3 .o file is in same folder as SeqFinder source code):

1. Download SeqFinder source code for Mac or Linux (in Repository)
2. Open terminal
3. CD to SeqFinder source code folder
4. Run command to compile SeqFinder: g++ -std=c++11 *.cpp -pthread sqlite3.o -o SeqFinder

Windows (Visual Studio 2017):

1. Download SeqFinder source for Windows (in Repository)
2. Open Visual Studio 2017
3. Create a New Project
4. Import the SeqFinder source code files
5. Go to Project->Properties and do the following:
   • Set Configuration to "All Configurations"
   • Set Platform to "All Platforms"
   • In Configuration Properties->VC++ Directories add C:\Path\To\sqlite3; to "Include Directories"
   • In Configuration Properties->VC++ Directories add C:\Path\To\sqlite; to "Include Libraries"
   • In C/C++->General add C:\Path\To\sqlite3; to "Additional Include Directories" and "Additional #using Directories"
   • In Linker->General add C:\Path\To\sqlite; to "Additional Library Directories"
   • In Linker->Input add C:\Path\To\sqlite\sqlite3.lib; in "Additonaly Dependencies
   • Make sure when you add these paths that there are ';' seperating all paths/object in the line.
6. For debugging, make sure Debug and x64 are selected before running
   • If debugging, make sure you set the debugging command arguments. See "How to run SeqFinder" below.
7. For compiling, make sure Release and x64 are selected before running

How to run SeqFinder

• CD to the directory containing the SeqFinder executable

  • The command line arguments for SeqFinder are as follows: `endonuclease pam multi_threading_bool 5_prime_pam_bool generate_repeats_file_bool 5_prime_length seed_length 3_prime_length org_code output_folder_path CASPERinfo_file_path input_file_path org_name notes on_target_data

• Example command: ./SeqFinder spCas9 NGG TRUE FALSE TRUE 4 16 0 org_code output_folder CASPERinfo input.fasta org_name notes DATA:CRISPRSCAN