chhylp123 / fmtree Goto Github PK
View Code? Open in Web Editor NEWFMtree: A fast locating algorithm of FM-indexes for genomic data
fmtree's People
Contributors
Stargazers
Watchers
fmtree's Issues
人基因组中，长模式 (len=30，Occ为1时，FMtree是否还有效？
程博士好，读了您的文章FMtree，很有收获. 我理解，当一个pattern有多个Occ时，FMtree将排位邻近的Occ一起做LF跳步，可以提高访问bwt串的数据局部性，即cache更有效，减少访存时间. 当人基因组中，取长30的模式时，绝大多数模式都只有1处Occ，这样的长模式，FMtree应该就起不到加速作用了. 看到文章中结果部分，FMtree仍比未优化的FM-index快了8倍，不太理解是什么原因？或者是我理解错了，FMtree是对多个（上千）模式的Occ一起处理？这样可以避免单个长模式Occ为1的情况.
FMTree,search报错
程博，按照您的论文，我将dna200MB经过preprocess处理，然后建了index，采样距离D=2。patterns也是从中随机抽取10个lengh=5的短字串。进行比对时候，就出现了如图所示的错误，这是怎么回事？
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.