We have developed GeneChaser, a gene structure prediction program, using a duration hidden markov model. GeneChaser consists of two major processes, one of which is to train datasets to produce parameter values and the other of which is to predict protein coding regions based on the parameter ...
The main computational biology problems with HMM-based solutions are protein family profiling, protein binding site recognition and the problem that is the topic of this paper, gene finding in DNA.Genefinding or gene prediction in DNA has become one of the foremost computational biology problems ...
Sequence-based protein function and structure prediction depends crucially on sequence-search sensitivity and accuracy of the resulting sequence alignments. We present an open-source, general-purpose tool that represents both query and database sequences by profile hidden Markov models (HMMs): 'HMM-HMM...
To improve tropism prediction accuracy, we developed two novel methods, the extreme gradient boosting based XGBpred and the hidden Markov model based HMMpred. Both XGBpred and HMMpred achieved higher specificities (72.56% and 72.09%) than the state-of-the-art methods Geno2pheno (61.6%) and G...
Background Structure prediction of membrane proteins is still a challenging computational problem. Hidden Markov models (HMM) have been successfully appli... P Fariselli,PL Martelli,R Casadio - 《Bmc Bioinformatics》 被引量: 134发表: 2005年 A computationally efficient approach to the estimation of ...
Approximately 30000 entries from the ITS2-DB, that uses a homology-based method for structure prediction, were re-annotated. We show that the method is able to correctly annotate an ITS2 as small as 58 nt from Giardia lamblia and an ITS2 as large as 1160 nt from humans. Thus, our ...