Fast Gene Sequence Search for Very Large Data File
Search for a specific sequence and record a neighboring code sequence with an offset position.
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- 팔로우하는 게시물 피드에서 업데이트를 확인할 수 있습니다
- 정보 수신 기본 설정에 따라 이메일을 받을 수 있습니다
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.
인용 양식
Binlin Wu (2026). Fast Gene Sequence Search for Very Large Data File (https://kr.mathworks.com/matlabcentral/fileexchange/31966-fast-gene-sequence-search-for-very-large-data-file), MATLAB Central File Exchange. 검색 날짜: .
