Reciprocal Blast for Windows

Complete set of scripts and applications to perform reciprocal Blast via BLAST+ utilities.

Requirements

The following must be installed on system:

• Microsoft C++ redistributable 2010
• Python 3+ (32 bit version)
• BioPython (available to download via pip)
• NCBI BLAST+ package installed
• xlsxwriter (available to download via pip) to parse procedure output
• Python interpreter py.exe set in PATH environment variable

Installation

Install requirements and simply copy the repository on your harddrive. Then copy executables from BLAST+ pakacge to tools/blast directory.

Usage

Performing reciprocal Blast

1. Put sequences in format .fasta or .fasta.gz. in the project_data directory. Files have to be put in the correct folders following the structure in the project_data -Example directory. Remember to set correct file extensions. Only .fasta or .fasta.gz are accepted.

2. Run GO.bat and enter the new workspace name. This script will manage entire procedure. If you want to do it manually go to point 3.

3. Run batch script process-data.bat. This will mask your protein and nucleotide sequences and copy them to the input_data directory.

4. Copy workspace_template and rename as you please. Remember to copy it to the same directory where workspace_template is.

5. Open your new workspace and run in the following order:

   • make_workspace.bat
   • run_blast.bat

Tuning data

After creating workspace with script make_workspace.bat you can edit local sequence source files as you wish, since they are only working copy. To create database from updated source sequences run make_blastdb.bat.

Obtaining output

All results are kept in the results directory. They are both in html and table formats. To convert output into more readable excel tables, there is a python utility tool in the path:

tools/mytools/processing/generate_tables.py

and its dependencies in the directory gen_lib. Simply copy the files in processing folder to the workspace and run from command line: py generate_tables.py results/species-name

Contact

This set of scripts was created for a science project. If you wish to see more features like:

• better documentation
• user-friendly interface
• no-nonsense fasta cutter
• automatic download of dependencies

Email me at : m.nowot@gmail.com