hidden markov model files Search Results


transmembrane structure tmhmm-2.0  (HealthTech Connex Inc)
90
HealthTech Connex Inc transmembrane structure tmhmm-2.0
Transmembrane Structure Tmhmm 2.0, supplied by HealthTech Connex Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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transmembrane structure tmhmm-2.0 - by Bioz Stars, 2026-06
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hiddenmarkov model  (Metrichor Ltd)
90
Metrichor Ltd hiddenmarkov model
Hiddenmarkov Model, supplied by Metrichor Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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hiddenmarkov model - by Bioz Stars, 2026-06
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markov random field modeling in computer vision  (Verlag GmbH)
90
Verlag GmbH markov random field modeling in computer vision
Markov Random Field Modeling In Computer Vision, supplied by Verlag GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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hidden markov model  (Celera)
90
Celera hidden markov model
Hidden Markov Model, supplied by Celera, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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hidden markov model - by Bioz Stars, 2026-06
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chromatin states defined by hidden markov models (hmm)  (Epigenomics ag)
90
Epigenomics ag chromatin states defined by hidden markov models (hmm)
Chromatin States Defined By Hidden Markov Models (Hmm), supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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chromatin states defined by hidden markov models (hmm) - by Bioz Stars, 2026-06
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hidden markov model (hmms)  (InterPro Inc)
90
InterPro Inc hidden markov model (hmms)
Hidden Markov Model (Hmms), supplied by InterPro Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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hidden markov model (hmms) - by Bioz Stars, 2026-06
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profile velvet hidden markov model  (InterPro Inc)
90
InterPro Inc profile velvet hidden markov model
Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden <t>Markov</t> model of velvet domain <t>PF11754</t> with 243 residues <t>(</t> <t>https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/</t> ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.
Profile Velvet Hidden Markov Model, supplied by InterPro Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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profile velvet hidden markov model - by Bioz Stars, 2026-06
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pfk-domain-hidden markov models  (InterPro Inc)
90
InterPro Inc pfk-domain-hidden markov models
Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden <t>Markov</t> model of velvet domain <t>PF11754</t> with 243 residues <t>(</t> <t>https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/</t> ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.
Pfk Domain Hidden Markov Models, supplied by InterPro Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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111 conserved single copy marker genes  (DuPont de Nemours)
90
DuPont de Nemours 111 conserved single copy marker genes
Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden <t>Markov</t> model of velvet domain <t>PF11754</t> with 243 residues <t>(</t> <t>https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/</t> ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.
111 Conserved Single Copy Marker Genes, supplied by DuPont de Nemours, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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profile hidden markov models (phmms) for the tetrahydrofolate dehydrogenase/cyclohydrolase, nad(p)-binding domain (pf02882.23, thf_dhg_cyh_c)  (InterPro Inc)
90
InterPro Inc profile hidden markov models (phmms) for the tetrahydrofolate dehydrogenase/cyclohydrolase, nad(p)-binding domain (pf02882.23, thf_dhg_cyh_c)
Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden <t>Markov</t> model of velvet domain <t>PF11754</t> with 243 residues <t>(</t> <t>https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/</t> ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.
Profile Hidden Markov Models (Phmms) For The Tetrahydrofolate Dehydrogenase/Cyclohydrolase, Nad(p) Binding Domain (Pf02882.23, Thf Dhg Cyh C), supplied by InterPro Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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profile hidden markov models (phmms) for the tetrahydrofolate dehydrogenase/cyclohydrolase, nad(p)-binding domain (pf02882.23, thf_dhg_cyh_c) - by Bioz Stars, 2026-06
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hidden markov models  (Lawrence Livermore National Security LLC)
90
Lawrence Livermore National Security LLC hidden markov models
Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden <t>Markov</t> model of velvet domain <t>PF11754</t> with 243 residues <t>(</t> <t>https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/</t> ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.
Hidden Markov Models, supplied by Lawrence Livermore National Security LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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hidden markov models - by Bioz Stars, 2026-06
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hidden markov model (tmhmm) posterior probability for transmembrane helix, inside, or outside  (HealthTech Connex Inc)
90
HealthTech Connex Inc hidden markov model (tmhmm) posterior probability for transmembrane helix, inside, or outside
Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden <t>Markov</t> model of velvet domain <t>PF11754</t> with 243 residues <t>(</t> <t>https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/</t> ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.
Hidden Markov Model (Tmhmm) Posterior Probability For Transmembrane Helix, Inside, Or Outside, supplied by HealthTech Connex Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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hidden markov model (tmhmm) posterior probability for transmembrane helix, inside, or outside - by Bioz Stars, 2026-06
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Image Search Results


Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden Markov model of velvet domain PF11754 with 243 residues ( https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/ ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.

Journal: Microbiology Spectrum

Article Title: Phylogenomics analysis of velvet regulators in the fungal kingdom

doi: 10.1128/spectrum.03717-23

Figure Lengend Snippet: Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden Markov model of velvet domain PF11754 with 243 residues ( https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/ ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.

Article Snippet: First, multiple alignments of protein sequences within each clade were constructed using HMMER 3.1 ( http://hmmer.org/ ) against the profile velvet hidden Markov model ( https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/ ) in InterPro ( ).

Techniques: Comparison, Sequencing, Residue