Transposon identification using profile HMMs

BMC Genomics

Research

Jun S Liu¹  Paul T Edlefsen¹ 

[1] Department of Statistics, Harvard University, One Oxford Street, Cambridge, MA, USA;

关键词: Hide Markov Model;    Training Sequence;    Conservation Level;    Profile Hide Markov Model;    Deletion State;   

DOI  :  10.1186/1471-2164-11-S1-S10

来源: Springer

【 摘 要 】

BackgroundTransposons are "jumping genes" that account for large quantities of repetitive content in genomes. They are known to affect transcriptional regulation in several different ways, and are implicated in many human diseases. Transposons are related to microRNAs and viruses, and many genes, pseudogenes, and gene promoters are derived from transposons or have origins in transposon-induced duplication. Modeling transposon-derived genomic content is difficult because they are poorly conserved. Profile hidden Markov models (profile HMMs), widely used for protein sequence family modeling, are rarely used for modeling DNA sequence families. The algorithm commonly used to estimate the parameters of profile HMMs, Baum-Welch, is prone to prematurely converge to local optima. The DNA domain is especially problematic for the Baum-Welch algorithm, since it has only four letters as opposed to the twenty residues of the amino acid alphabet.ResultsWe demonstrate with a simulation study and with an application to modeling the MIR family of transposons that two recently introduced methods, Conditional Baum-Welch and Dynamic Model Surgery, achieve better estimates of the parameters of profile HMMs across a range of conditions.ConclusionsWe argue that these new algorithms expand the range of potential applications of profile HMMs to many important DNA sequence family modeling problems, including that of searching for and modeling the virus-like transposons that are found in all known genomes.

【 授权许可】

CC BY   
© Edlefsen and Liu; licensee BioMed Central Ltd. 2010