• HMMER

  • Referenced in 19 articles [sw10514]
  • make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER ... sequence, multiple protein sequence alignment or profile HMM against a target sequence database...
  • AFP-Pred

  • Referenced in 24 articles [sw22441]
  • Pred was compared with BLAST and HMM. High prediction accuracy and successful of prediction...
  • HTK

  • Referenced in 15 articles [sw07937]
  • tools provide sophisticated facilities for speech analysis, HMM training, testing and results analysis. The software ... used to build complex HMM systems. The HTK release contains extensive documentation and examples...
  • hmm

  • Referenced in 14 articles [sw05422]
  • hidden Markov model (HMM) is one in which you observe a sequence of emissions...
  • TileMap

  • Referenced in 14 articles [sw35530]
  • method (MA) or a hidden Markov model (HMM). Unbalanced mixture subtraction is proposed to provide ... rate for MA and model parameters for HMM. Availability: TileMap is freely available...
  • R/qtl

  • Referenced in 13 articles [sw20451]
  • mapping is the hidden Markov model (HMM) technology for dealing with missing genotype data ... have implemented the main HMM algorithms, with allowance for the presence of genotyping errors...
  • Infernal

  • Referenced in 12 articles [sw17000]
  • based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods...
  • SRN/HMM

  • Referenced in 9 articles [sw02952]
  • network(SRN) and the hidden Markov models(HMM) are combined in this approach. The improved ... regarded as the states of HMM, and the Lattice Viterbi algorithm is employed to search ... best word sequence in the HMM framework. Experimental results show SRN/HMM approach has better performance ... than the standard HMM...
  • PennCNV

  • Referenced in 16 articles [sw19390]
  • present PennCNV, a hidden Markov model (HMM) based approach, for kilobase-resolution detection of CNVs...
  • EasyGene

  • Referenced in 7 articles [sw17322]
  • based on a hidden Markov model (HMM) that is automatically estimated for a new genome ... genome and used to estimate the HMM. Putative genes are then scored with ... HMM, and based on score and length of an ORF, the statistical significance is calculated...
  • momentuHMM

  • Referenced in 8 articles [sw21676]
  • addresses many of the deficiencies in existing HMM software. Features include: 1) data pre-processing ... momentuHMM considerably extends the capabilities of existing HMM software while accounting for common challenges associated...
  • HMM-DM

  • Referenced in 4 articles [sw23510]
  • HMM-DM: identifying differentially methylated regions using a hidden Markov model. DNA methylation ... have developed a new approach named HMM-DM to detect DM regions between two biological ... approach first uses a hidden Markov model (HMM) to identify DM CG sites accounting ... BSmooth. We also illustrate the application of HMM-DM using a real breast cancer dataset...
  • KinasePhos

  • Referenced in 8 articles [sw22468]
  • KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific...
  • Julius

  • Referenced in 5 articles [sw21656]
  • word N-gram and context-dependent HMM, it can perform real-time decoding on various ... from model structures, and wide variety of HMM structures are supported such as shared-state...
  • HMM

  • Referenced in 4 articles [sw11733]
  • package HMM: HMM - Hidden Markov Models. Easy to use library to setup, apply and make...
  • HMM-Fisher

  • Referenced in 4 articles [sw28769]
  • HMM-Fisher program identifies differentially methylated (DM) CG sites (DMCs) and regions (DMRs) from whole ... outputs identified DM CG sites and regions. HMM-Fisher requires R installed. Ideally...
  • RepeatMasker

  • Referenced in 7 articles [sw17266]
  • repeats and currently supports Dfam ( profile HMM library derived from Repbase sequences ) and Repbase...
  • GeneScout

  • Referenced in 7 articles [sw31815]
  • junction donor and acceptor sites, etc. An HMM model is also proposed for exon coding...
  • HPeak

  • Referenced in 4 articles [sw29576]
  • HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. Results ... introduce HPeak, a H idden Markov model (HMM)-based Peak-finding algorithm for analyzing ChIP...
  • MedPost

  • Referenced in 3 articles [sw07991]
  • speech tagger employing a hidden Markov model (HMM) to combine contextual information with lexical information ... transition probabilities. The output probabilities of the HMM are determined for words in the lexicon ... most likely tag sequence in the HMM matching the tokens. MedPost was trained specifically...