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Fast Gene Sequence Search for Very Large Data File

version (3.85 KB) by Binlin Wu
Search for a specific sequence and record a neighboring code sequence with an offset position.


Updated 01 Jul 2011

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A research fellow at Harvard asked me to write a program to search for gene sequence, such as ‘TCC’, and record the next 4 codes. The data file was 14Gb. He tried some matlab codes, and the system froze, or kept running and never stopped.

I first tested using a loop method (V1.0). It turned out it would take a month to finish 14Gb data on my 1.8GHz Core 2 Duo/3Gb RAM PC. Then I updated it to use matrix. It turned out it would only take 1.3 hours on my 1.8Gb PC or 40 minutes on my 2.33GHz Core 2 Duo/2Gb RAM PC. It beat any codes that he got using Python or other languages.

I put the file here, and hopefully it will be useful to the people with the same situation.

Cite As

Binlin Wu (2020). Fast Gene Sequence Search for Very Large Data File (, MATLAB Central File Exchange. Retrieved .

Comments and Ratings (2)


well done , nice work

Binlin Wu

Any comment or feedback is welcome.


Function renamed and all names made consistent.

Added a parameter nHL, which is used to specify how many headlines you want to remove from the data. It is 0 by default.

MATLAB Release Compatibility
Created with R2010b
Compatible with any release
Platform Compatibility
Windows macOS Linux