How do I read large FASTA files into MATLAB using BioInformatics toolbox 2.1.1 (R14SP3)?

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MathWorks Support Team 2009-6-27

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https://ww2.mathworks.cn/matlabcentral/answers/92473-how-do-i-read-large-fasta-files-into-matlab-using-bioinformatics-toolbox-2-1-1-r14sp3

I have a very large FASTA file that I am trying to read into MATLAB using the FASTAREAD function from the BioInformatics toolbox 2.1.1 (R14SP3). However, when I try to do so, initially MATLAB freezes and slowly the system stops responding.

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Answer 1

MathWorks Support Team 2009-6-27

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https://ww2.mathworks.cn/matlabcentral/answers/92473-how-do-i-read-large-fasta-files-into-matlab-using-bioinformatics-toolbox-2-1-1-r14sp3#answer_101824

splitlargefasta.m

You can observe this behavior when the size of the FASTA file is too big for MATLAB to handle. To workaround this issue, you can split a big FASTA file into smaller pieces and use the FASTAREAD function to read the smaller files into MATLAB.

The utility to split FASTA files into smaller pieces is attached to this document.