StochHMM: a flexible hidden Markov model tool and C plus plus library

被引：11

作者：

Lott, Paul C. ^{[1
]}

Korf, Ian ^{[1
]}

机构：

[1] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA

来源：

BIOINFORMATICS | 2014年 / 30卷 / 11期

基金：

美国国家卫生研究院;

关键词：

R-LOOP FORMATION; PREDICTION;

D O I：

10.1093/bioinformatics/btu057

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Hidden Markov models (HMMs) are probabilistic models that are well-suited to solve many different classification problems in computation biology. StochHMM provides a command-line program and C++ library that can implement a traditional HMM from a simple text file. StochHMM provides researchers the flexibility to create higher-order emissions, integrate additional data sources and/or user-defined functions into multiple points within the HMM framework. Additional features include user-defined alphabets, ability to handle ambiguous characters in an emission-dependent manner, user-defined weighting of state paths and ability to tie transition probabilities to sequence.

引用

页码：1625 / 1626

页数：2

共 13 条

[1]

[Anonymous], BIOINFORMATICS ALGOR

[2] HMM sampling and applications to gene finding and alternative splicing [J].

Cawley, Simon L. ;

Pachter, Lior .

BIOINFORMATICS, 2003, 19 :II36-II41

[3] GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination [J].

Ginno, Paul A. ;

Lim, Yoong Wearn ;

Lott, Paul L. ;

Korf, Ian ;

Chedin, Frederic .

GENOME RESEARCH, 2013, 23 (10) :1590-1600

[4] R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters [J].

Ginno, Paul A. ;

Lott, Paul L. ;

Christensen, Holly C. ;

Korf, Ian ;

Chedin, Frederic .

MOLECULAR CELL, 2012, 45 (06) :814-825

[5]

Kulp D, 1996, Proc Int Conf Intell Syst Mol Biol, V4, P134

[6] HMMConverter 1.0: a toolbox for hidden Markov models [J].

Lam, Tin Yin ;

Meyer, Irmtraud M. .

NUCLEIC ACIDS RESEARCH, 2009, 37 (21) :e139-e139

[7] HMMoC - a compiler for hidden Markov models [J].

Lunter, Gerton .

BIOINFORMATICS, 2007, 23 (18) :2485-2487

[8]

Sand A., 2010, Proceedings 2010 9th International Workshop on Parallel & Distributed Methods in Verification and 2nd International Workshop on High Performance Computational Systems Biology (PDMC-HiBi 2010), P126, DOI 10.1109/PDMC-HiBi.2010.24

[9] The human placenta methylome [J].