Fast Gene Sequence Search for Very Large Data File

版本 1.6.0.0 (3.9 KB) 作者: Binlin Wu
Search for a specific sequence and record a neighboring code sequence with an offset position.
0.0
(0)
262.0 次下载
更新时间 2011/7/1

查看许可证

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.

引用格式

Binlin Wu (2024). Fast Gene Sequence Search for Very Large Data File (https://www.mathworks.com/matlabcentral/fileexchange/31966-fast-gene-sequence-search-for-very-large-data-file), MATLAB Central File Exchange. 检索来源 .

MATLAB 版本兼容性
创建方式 R2010b
兼容任何版本
平台兼容性
Windows macOS Linux
类别
在 Help Center 和 MATLAB Answers 中查找有关 Large Files and Big Data 的更多信息

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

版本 已发布 发行说明
1.6.0.0

Function renamed and all names made consistent.
1.2.0.0

Added a parameter nHL, which is used to specify how many headlines you want to remove from the data. It is 0 by default.
1.0.0.0