Fasta File Splitter

Console application that reads a protein FASTA file and splits it apart into a number of sections. Although the splitting is random, each section will have a nearly identical number of residues.


Use the Fasta File Splitter program to break apart a large protein FASTA file into a series of smaller FASTA files, all equally sized. Specify the number of sections using /N. Example usage:

FastaFileSplitter.exe H_sapiens_IPI_2008-02-07.fasta /N:25



All publications that utilize this software should provide appropriate acknowledgement to PNNL and the Fasta-File-Splitter GitHub repository. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.


These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

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