Keywords: HMM، مدل پنهان مارکوف; LBD, Lateral Boundary Domain; LOB, Lateral Organ Boundary gene; HMM, Hidden Markov model; NJ, neighbor-joining; GSDS, Gene Structure Display Server; MEME, Multiple Em For Motif Elicitation; PKM, The reads per kilobase of exon model per million mapped read
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Keywords: HMM، مدل پنهان مارکوف; DNA, deoxyribonucleic acid; HMM, hidden Markov model; LTR, long terminal repeat; PCR, polymerase chain reaction; PHD, plant homeodomain; poly(A), polyadenilation; RNA, ribonucleic acid; RT, reverse transcription; SMC, structural maintenance of chromosome;
Keywords: HMM، مدل پنهان مارکوف; Antibiotics; Biosynthesis; Bioinformatics; NRPS; PKS; Natural productA, adenylation domain; BGC, biosynthetic gene cluster; C, condensation domain; GPR, gene-protein-reaction; HMM, hidden Markov model; LC, liquid chromatography; MS, mass spectrometry; NMR
Keywords: HMM، مدل پنهان مارکوف; AP, aspartic protease; Asp, aspartate; HMM, Hidden Markov Model; RVP, retroviral protease; API, aspartic peptidase inhibitor; TSA, Taenia saginata; TAS, Taenia asiatica; HmN, Hymenolepis microstoma; EmuJ, Echinococcus multilocularis; Egr, Echinococcus gra
Keywords: HMM، مدل پنهان مارکوف; AIC, Akaike's Information Criterion; ARS, area-restricted search; BMR, basal metabolic rate; CPF, central place forager; FlMR, metabolic rate while in flight; FMR, field metabolic rate; GPS, global positioning system; HMM, Hidden Markov model; RMR, restin
Genome-wide analysis of WRKY family of transcription factors in common bean, Phaseolus vulgaris: Chromosomal localization, structure, evolution and expression divergence
Keywords: HMM، مدل پنهان مارکوف; TFs, transcription factors; RNA-seq, RNA sequencing; HMM, hidden Markov model; MW, molecular weight; pI, isoelectric point; aa, amino acid(s); AtWRKY, WRKY transcription factors in Arabidopsis; PvWRKYs, WRKY transcription factors in Phaseolus vulgaris; P.
Genome-wide identification, classification and expression analysis of the PHD-finger protein family in Populus trichocarpa
Keywords: HMM، مدل پنهان مارکوف; PHD, plant homeobox domain; pI, isoelectric point; Mya, million years ago; CDS, coding sequences; HMM, hidden Markov model; NJ, neighbor-joining; At, Arabidopsis thaliana; Pt, Populus trichocarpa; GEO, Gene Expression Omnibus; NCBI, National Center for Bi
Genome-wide comparative analysis of ABC systems in the Bdellovibrio-and-like organisms
Keywords: HMM، مدل پنهان مارکوف; BALOs, Bdellovibrio-and-like organisms; ABC, ATP-binding cassette; BD, Bdellovibrio; Bx, Bacteriovorax; HMM, Hidden Markov Model; SMART, Simple Modular Architecture Research Tool; CDD, Conserved Domain DatabaseABC transporter; BALOs; Bacteriovorax; Bdello
In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines
Keywords: HMM، مدل پنهان مارکوف; ATM, ataxia telangiectasia mutated; BRAF, B-Raf; CFTR, cystic fibrosis transmembrane conductance regulator; GalNAc-T1, N-acetylgalactosaminyltransferase 1; GATK, Genome Analysis Tool Kit; HBB, hemoglobin beta; HMM, Hidden Markov Model; IGF1R, insulin-like
Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata
Keywords: HMM، مدل پنهان مارکوف; TFs, transcription factors; WGT, whole-genome triplication; RNA-seq, RNA sequencing; NCBI, National Center for Biotechnology Information; SRA, Sequence Read Archive; HMM, hidden Markov model; MW, molecular weight; pI, isoelectric point; aa, amino acid(s);
Genome-wide identification and analysis of the MADS-box gene family in sesame
Keywords: HMM، مدل پنهان مارکوف; AGL, AGAMOUS-like; ANR, anthocyanidin reductase; FLC, FLOWERING LOCUS C; FT, FLOWERING LOCUS T; HMM, hidden Markov model; LFY, LEAFY; LG, linkage group; ML, maximum-likelihood; NJ, neighbor-joining; ORF, open reading frame; PI, PISTILLATA; SOC1, suppresso
Proteome-scale identification and characterization of mitochondria targeting proteins of Mycobacterium avium subspecies paratuberculosis: Potential virulence factors modulating host mitochondrial function
Keywords: HMM، مدل پنهان مارکوف; BPP, Binary Profile of Pattern; DBETH, Database of Bacterial Exotoxins for Human; EMBL, European Molecular Biology Laboratory; FAST-ALL, FASTA; GSP, General Secretory Pathway; HMM, Hidden Markov Model; HMMTOP, Hidden Markov Model for Topology Prediction;
Haplotype-based approach for noninvasive prenatal diagnosis of congenital adrenal hyperplasia by maternal plasma DNA sequencing
Keywords: HMM، مدل پنهان مارکوف; CAH, congenital adrenal hyperplasia; HMM, hidden Markov model; 21-OHD, 21-hydroxylase deficiency; CVS, chorionic villus sampling; cff-DNA, cell-free fetal DNA; NIPT, noninvasive prenatal testing; 17-OHP, 17-hydroxyprogesterone; ACTH, adrenocorticotropic h
A male-specific QTL for social interaction behavior in mice mapped with automated pattern detection by a hidden Markov model incorporated into newly developed freeware
Keywords: HMM، مدل پنهان مارکوف; QTL, quantitative trait locus; HMM, hidden Markov model; CSV, comma-separated values; FLV, Flash video; AVI, Audio video interleave; ANOVA, analyses of varianceSocial interaction; Mouse; Consomic strain; Behavior genetics; Aggression
Novel genes that mediate nuclear respiratory factor 1-regualted neurite outgrowth in neuroblastoma IMR-32 cells
Keywords: HMM، مدل پنهان مارکوف; NRF-1, nuclear respiratory factor 1; NRE, NRF-1 response element; EMSA, gel electrophoretic mobility shift assays; ChIP, chromatin immunoprecipitation; HMM, hidden Markov Model; shRNA, short hairpin RNA; CDCA7L, cell division cycle associated 7-like; MAPR
Genome-wide identification and expression analysis of MAPK and MAPKK gene family in Malus domestica
Keywords: HMM، مدل پنهان مارکوف; MAPK, mitogen-activated protein kinase; MAPKK, MAPK kinase; BLAST, Basic Local Alignment Search Tool; GWD, Genome-Wide Duplication; HMM, Hidden Markov Model; MEGA, Molecular Evolutionary Genetics Analysis; MUSCLE, Multiple Sequence Comparison by Log-Expec
A genome-wide analysis of the RNA helicase gene family in Solanum lycopersicum
Keywords: HMM، مدل پنهان مارکوف; SF2, superfamily 2; CSS, conserved syntenic segments; BLAST, the Basic Local Alignment Search Tool; SMART, a Simple Modular Architecture Research Tool; HMM, Hidden Markov Model; MUSCEL, Multiple Sequence Comparison by Log-Expectation; NJ, the neighbor-joi
Protein complex prediction based on maximum matching with domain–domain interaction
Keywords: HMM، مدل پنهان مارکوف; DDI, domain–domain interaction; HMM, hidden Markov model; PPI, protein–protein interaction; MCL, Markov clusteringDomain–domain interaction; Maximum matching; Protein complex; Protein–protein interaction
Hydroxysteroid dehydrogenases (HSDs) in bacteria – A bioinformatic perspective
Keywords: HMM، مدل پنهان مارکوف; HMM, hidden Markov model; SDR, short-chain dehydrogenase/reductase; HSDs, hydroxysteroid dehydrogenasesShort-chain dehydrogenases/reductases (SDR); Hidden Markov model; Phylogenetic analysis; Bioinformatic approach; Bacteria; Hydroxysteroid dehydrogenases
Bioinformatic and biochemical characterization of DCXR and DHRS2/4 from Caenorhabditis elegans
Keywords: HMM، مدل پنهان مارکوف; DCXR, dicarbonyl/l-xylulose reductase; DHRS, dehydrogenase/reductase; HMM, hidden Markov model; SDR, short-chain dehydrogenase/reductase; DMSO, dimethyl sulfoxide; FPLC, fast protein liquid chromatographyCarbonyl reduction; Short-chain dehydrogenases/redu
The Evolution and Structure Prediction of Coiled Coils across All Genomes
Keywords: HMM، مدل پنهان مارکوف; KIH, knobs-into-holes; HMM, hidden Markov model; PDB, Protein Data Bank; 3D, three-dimensional; LUCA, last universal common ancestor of lifeprotein evolution; coiled coil; hidden Markov model; protein structure; SUPERFAMILY
The phylogeny of orthoretroviral long terminal repeats (LTRs)
Keywords: HMM، مدل پنهان مارکوف; LTR, long terminal repeat; HMM, Hidden Markov Model; MMTV, Mouse Mammary Tumor Virus; HML, human MMTV-like; HERV, human endogenous retrovirus; pol, polymerase gene nucleotide sequence; Pol, polymerase gene amino-acid sequence; Gag, group antigen amino-aci
5.8S-28S rRNA interaction and HMM-based ITS2 annotation
Keywords: HMM، مدل پنهان مارکوف; bp, basepairs; CBC, compensatory base change; C2-site, cleavage site 2; HMM, Hidden Markov Model; ITS2, Internal Transcribed Spacer 2; LSU, large subunit; nt, nucleotides; rRNA, ribosomal RNA; SSU, small subunitHidden Markov models; Internal transcribed s
Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics
Keywords: HMM، مدل پنهان مارکوف; SBP, sugar-beet pectin; GalA, galacturonic acid; PGA, polygalacturonic acid; HMM, hidden Markov model; ORF, open reading frameAspergillus niger; Functional genomics; Transcriptomics; Pectin degradation; Enzyme network
Structural and Functional Diversity of Novel Coronin 1C (CRN2) Isoforms in Muscle
Keywords: HMM، مدل پنهان مارکوف; mAb, monoclonal antibody; RT, reverse transcription; EST, expressed sequence tag; NCBI, National Center for Biotechnology Information; TSS, transcription start site; ChIP, chromatin immunoprecipitation; HMM, hidden Markov model; RLM, RNA-ligase-mediatedCR
Histone Deacetylases Regulate Multicellular Development in the Social Amoeba Dictyostelium discoideum
Keywords: HMM، مدل پنهان مارکوف; HDAC, histone deacetylase; HAT, histone acetyltransferase; HMM, hidden Markov model; TSA, trichostatin A; RT-PCR, reverse transcription-polymerase chain reaction; HDAH, histone deacetylase-like amidohydrolase; HDLP, histone deacetylase-like proteinhistone
Structural Alphabets for Protein Structure Classification: A Comparison Study
Keywords: HMM، مدل پنهان مارکوف; 3D, three-dimensional; NS, native sequence; SSES, secondary-structure element sequence; LFS, local fragment sequence; GFS, global fragment sequence; SVM, support vector machine; HMM, hidden Markov model; cRMS, coordinate root mean square; MDS, multidimens
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets
Keywords: HMM، مدل پنهان مارکوف; TE, Transposable elements; RU, Repbase update; LTR, Long terminal repeat; HMM, Hidden markov model; CI, Consistency index; MinGL, Minimal gap length; MaxND, Maximal nucleotide densityTransposable elements; Repbase Update; Genome annotation; Arabidopsis th
Species-specific expansion of C2H2 zinc-finger genes and their expression profiles in silkworm, Bombyx mori
Keywords: HMM، مدل پنهان مارکوف; C2H2 zinc-finger; Transcription factor; Metamorphism; Development; Expression pattern; Bombyx moriZFP, zinc-finger protein; C2H2, Cys(2)/His(2); EST, expressed sequence tag; HMM, hidden Markov model; fru, fruitless; BR-C, Broad-Complex gene; WGS, Whole Ge
Molecular evolution of the MLO gene family in Oryza sativa and their functional divergence
Keywords: HMM، مدل پنهان مارکوف; cDNA, complementary to RNA; CDS, coding DNA sequence; dN/dS, ratio of nonsynonymous-to-synonymous substitutions; EST, expressed sequence tag; GEO, gene expression omnibus; HMM, hidden Markov model; KOME, Knowledge-based Oryza Molecular biological Encyclop
Diversification and adaptive evolution of putative sweet taste receptors in threespine stickleback
Keywords: HMM، مدل پنهان مارکوف; T1R, taste receptor family 1; T2R, taste receptor family 2; HMM, hidden Markov model; ML, maximum likelihood; LRT, likelihood ratio test; TM, transmembrane.Sense of taste; Gene duplication; Positive selection; Multigene family
Unsupervised word sense disambiguation for Korean through the acyclic weighted digraph using corpus and dictionary
Keywords: HMM، مدل پنهان مارکوف; AWD, Acyclic weighted digraph; HMM, Hidden Markov model; MRD, Machine-readable dictionary; POS, Part of speech; WSD, Word sense disambiguationAcyclic weighted digraph; Machine-readable dictionary; Viterbi algorithm; Word sense disambiguation
Identification of a Single HNH Active Site in Type IIS Restriction Endonuclease Eco31I
Keywords: HMM، مدل پنهان مارکوف; REase, restriction endonuclease; wt, wild-type; aa, amino acid residue(s); HMM, hidden Markov model; ds, double-strandedrestriction endonuclease; type IIS; HNH; endonuclease VII; active site
Apo and Calcium-bound Crystal Structures of Alpha-11 Giardin, an Unusual Annexin from Giardia lamblia
Keywords: HMM، مدل پنهان مارکوف; MAD, multi-wavelength anomalous dispersion; HMM, hidden Markov model; PS, phosphatidylserine; PC, phosphatidylcholine; HTS, heparin-derived tetrasaccharide; POPS, 1-palmitoyl-2-oleoyl-sn-glycero-3- [phospho-l-serine]; POPC, 1-palmitoyl-2-oleoyl-sn-glycero
Multivariate Analysis of Conserved Sequence–Structure Relationships in Kinesins: Coupling of the Active Site and a Tubulin-binding Sub-domain
Keywords: HMM، مدل پنهان مارکوف; cryoEM, cryo-electron microscopy; PCA, principal component analysis; HMM, hidden Markov model; SCA, statistical coupling analysis; RMSF, root mean square fluctuation; PDB, protein data bankkinesin; molecular motors; sequence analysis; structure analysis;
Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus
Keywords: HMM، مدل پنهان مارکوف; NRPS, non-ribosomal peptide synthetase; NRPs, non-ribosomal peptides; A domain, adenylation domain; T domain, peptidyl carrier domain; C domain, condensation domain; TE, thioesterase domain; HMM, hidden Markov model; NJ, neighbor-joining; DMEM, Dulbecco's
A computational prediction of isochores based on hidden Markov models
Keywords: HMM، مدل پنهان مارکوف; HMM, hidden Markov Model; G+C, guanine plus cytosine content; G+C3, G+C content of the third codon position; bp, base pair; kb, kilobase pair; Mb, megabase pair; UTR, untranslated regions; CDS, coding sequencesIsochores; Genome; Markov; Model
Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse
Keywords: HMM، مدل پنهان مارکوف; GPCR; Glutamate; Rhodopsin; Adhesion; Frizzled; Taste2; SecretinBLAST, basic local alignment search tool; BLAT, BLAST-like alignment tool; EST, expressed sequence tag; GPCR, G protein-coupled receptor; HMM, Hidden Markov model; MP, maximum parsimony; RPS-
Fault recognition method for speed-up and speed-down process of rotating machinery based on independent component analysis and Factorial Hidden Markov Model
Keywords: HMM، مدل پنهان مارکوف; FHMM, Factorial Hidden Markov Model; HMM, Hidden Markov Model; ICA, Independent Component Analysis; ICA–FHMM, a fault recognition method, in which ICA is used for a feature extraction, and FHMM, as a classifier; ICA–HMM, a fault recognition method in whic
The C-terminal TPR Domain of Tom70 Defines a Family of Mitochondrial Protein Import Receptors Found only in Animals and Fungi
Keywords: HMM، مدل پنهان مارکوف; protein import; tetratricopeptide repeat; Tom70; Tom71; hidden Markov modelsTOM, translocase in the outer mitochondrial membrane; TIM, translocase in the inner mitochondrial membrane; TPR, tetratricopeptide repeat; HMM, hidden Markov model; CCCP, m-chloro
Prediction of Binding Sites of Peptide Recognition Domains: An Application on Grb2 and SAP SH2 Domains
Keywords: HMM، مدل پنهان مارکوف; binding site motif; MM/PBSA; protein–protein interactions; SH2 domainSH2, Src homology 2; SAP, SLAM-associated protein; HMM, hidden Markov model
Unsupervised word sense disambiguation for Korean through the acyclic weighted digraph using corpus and dictionary
Keywords: HMM، مدل پنهان مارکوف; AWD, Acyclic weighted digraph; HMM, Hidden Markov model; MRD, Machine-readable dictionary; POS, Part of speech; WSD, Word sense disambiguationAcyclic weighted digraph; Machine-readable dictionary; Viterbi algorithm; Word sense disambiguation
Trypanosoma cruzi: Analysis of the complete PUF RNA-binding protein family
Keywords: HMM، مدل پنهان مارکوف; Post-transcriptional regulation; Bioinformatics analysis; Yeast three hybrids; Chagas disease; NRE, nanos response element; UTR, untranslated region; HMM, hidden Markov model; ORF, open reading frame; aa, amino acids; TriTryp, Trypanosoma brucei, Trypanos
Efficient spike-sorting of multi-state neurons using inter-spike intervals information
Keywords: HMM، مدل پنهان مارکوف; DHPG, (S)-3,5-dihydroxyphenylglycine; HMM, hidden Markov model; ISI, inter-spike interval; MC, Monte Carlo; MCMC, Markov chain Monte Carlo; mGluR1, group 1 metabotropic glutamate receptor; PC, Purkinje cell; REM, replica exchange method; S.D., standard de
User-customized password speaker verification using multiple reference and background models
Keywords: HMM، مدل پنهان مارکوف; SV, speaker verification; TD, text-dependent; TI, text-independent; MLP, Multi-Layer Perceptron; SI-MLP, speaker-independent multi-layer perceptron; EER, equal error rate; GMM, Gaussian Mixture Model; HMM, Hidden Markov Model; HMM/MLP, Hybrid Hidden Marko
Evolution of Structure and Function in the o-Succinylbenzoate Synthase/N-Acylamino Acid Racemase Family of the Enolase Superfamily
Keywords: HMM، مدل پنهان مارکوف; OSBS/NAAAR, o-succinylbenzoate synthase/N-acylamino acid racemase; MLE, muconate lactonizing enzyme; nr, non-redundant; HMM, Hidden Markov Model; AEE, L-Ala-D/L-Glu epimeraseenolase superfamily; protein evolution; mechanistically diverse superfamily; subs