HMMoC - a compiler for hidden Markov models

被引：24

作者：

Lunter, Gerton ^{[1
]}

机构：

[1] Univ Oxford, Dept Physiol Anat & Genet, MRC Funct Genet Unit, Oxford OX1 3TG, England

来源：

BIOINFORMATICS | 2007年 / 23卷 / 18期

基金：

英国医学研究理事会;

关键词：

D O I：

10.1093/bioinformatics/btm350

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Hidden Markov models are widely applied within computational biology. The large data sets and complex models involved demand optimized implementations, while efficient exploration of model space requires rapid prototyping. These requirements are not met by existing solutions, and hand-coding is timeconsuming and error- prone. Here, I present a compiler that takes over the mechanical process of implementing HMM algorithms, by translating high- level XML descriptions into efficient C++ implementations. The compiler is highly customizable, produces efficient and bug- free code, and includes several optimizations.

引用

页码：2485 / 2487

页数：3

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