HMMER Profile File Format
The profile hidden Markov Model (HMM) calculated from multiple sequence alignment data in this service is stored in Profile HMM save format (usually with ".hmm" extension). It is an ASCII file containing a lot of header and descriptive records followed by large numerical matrix which holds a probabilistic model of the motif. The file of this format is useful to search against sequence databases to find other proteins which share the same motif.
Description
More detailed information about this field from each metasource.
The profile hidden Markov Model (HMM) calculated from multiple sequence alignment data in this service is stored in Profile HMM save format (usually with ".hmm" extension). It is an ASCII file containing a lot of header and descriptive records followed by large numerical matrix which holds a probabilistic model of the motif. The file of this format is useful to search against sequence databases to find other proteins which share the same motif.
metasource: Fairsharing.orgversion: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
Webpage:
http://www.hmmer.orgWebpage
More detailed information about this field from each metasource.
http://www.hmmer.org
metasource: Fairsharing.orgversion: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
HMMER web server: 2015 update
PMID: 25943547
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
PMID: 15831105
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
Publications
More detailed information about this field from each metasource.
HMMER web server: 2015 update
PMID: 25943547
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
PMID: 15831105
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
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HMMER web server: 2015 update
PubMed citations: 395.
395 articles citing: HMMER web server: 2015 update
Novel Salmonella Phage, vB_Sen_STGO-35-1, Characterization and Evaluation in Chicken Meat. PMID:35336181
Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes. PMID:35322069
Genome-wide characterization and expression analysis of Erf gene family in cotton. PMID:35317739
BmPMFBP1 regulates the development of eupyrene sperm in the silkworm, Bombyx mori. PMID:35312700
Genome-Wide Identification and Expression Profiling of Germin-Like Proteins Reveal Their Role in Regulating Abiotic Stress Response in Potato. PMID:35251067
A Highly Specific Holin-Mediated Mechanism Facilitates the Secretion of Lethal Toxin TcsL in Paeniclostridiumsordellii. PMID:35202151
Integrated Analysis of Transcriptome and Proteome to Reveal Pupal Color Switch in Papilio xuthus Butterflies. PMID:35186009
Identification of bZIP transcription factors and their responses to brown spot in pear. PMID:35099498
MrTPS3 and MrTPS20 Are Responsible for β-Caryophyllene and α-Pinene Production, Respectively, in Red Bayberry (Morella rubra). PMID:35069655
Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon. PMID:35054827
Heat shock transcription factor (Hsf) gene family in common bean (Phaseolus vulgaris): genome-wide identification, phylogeny, evolutionary expansion and expression analyses at the sprout stage under abiotic stress. PMID:35031009
Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding. PMID:35025730
Genome-wide identification and expression analysis of NtbHLH gene family in tobacco (Nicotiana tabacum) and the role of NtbHLH86 in drought adaptation. PMID:35024520
An antimicrobial peptide specifically active against Listeria monocytogenes is secreted by Bacillus pumilus SF214. PMID:34979918
The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota L-carnitine catabolism. PMID:34949826
Genome-wide Identification and Evolution of the PP2C Gene Family in Eight Rosaceae Species and Expression Analysis Under Stress in Pyrus bretschneideri. PMID:34858482
Hidden neural networks for transmembrane protein topology prediction. PMID:34849210
A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes. PMID:34795236
Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria. PMID:34730808
Novel Binding Partners for CCT and PhLP1 Suggest a Common Folding Mechanism for WD40 Proteins with a 7-Bladed Beta-Propeller Structure. PMID:34698247
Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris. PMID:34629769
Genome-Wide Characterization of Glutathione Peroxidase (GPX) Gene Family in Rapeseed (Brassica napus L.) Revealed Their Role in Multiple Abiotic Stress Response and Hormone Signaling. PMID:34573113
Nicastrin-Like, a Novel Transmembrane Protein from Trypanosoma cruzi Associated to the Flagellar Pocket. PMID:34442829
Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions. PMID:34439430
Synergistic stabilization of a double mutant in chymotrypsin inhibitor 2 from a library screen in E. coli. PMID:34408246
Structural and mechanistic basis for protein glutamylation by the kinase fold. PMID:34407442
CASPredict: a web service for identifying Cas proteins. PMID:34395100
Genome-wide identification of serine acetyltransferase (SAT) gene family in rice (Oryza sativa) and their expressions under salt stress. PMID:34389920
RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content. PMID:34286299
Characterisation of Bacteriophage-Encoded Depolymerases Selective for Key Klebsiella pneumoniae Capsular Exopolysaccharides. PMID:34222050
Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus. PMID:34201869
NOD: a web server to predict New use of Old Drugs to facilitate drug repurposing. PMID:34188160
Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum. PMID:34155201
Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction. PMID:34139218
A phylogenetic approach for weighting genetic sequences. PMID:34049487
Repurposing of synaptonemal complex proteins for kinetochores in Kinetoplastida. PMID:34006126
A family of pathogen-induced cysteine-rich transmembrane proteins is involved in plant disease resistance. PMID:33856567
Origin and evolution of nonulosonic acid synthases and their relationship with bacterial pathogenicity revealed by a large-scale phylogenetic analysis. PMID:33848237
Genomic Characterization and Expression Analysis of the SnRK Family Genes in Dendrobium officinale Kimura et Migo (Orchidaceae). PMID:33802577
Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data. PMID:33795009
The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista. PMID:33740894
Biodiversity of New Lytic Bacteriophages Infecting Shigella spp. in Freshwater Environment. PMID:33679642
Genome-wide identification of Ran GTPase family genes from wheat (T. aestivum) and their expression profile during developmental stages and abiotic stress conditions. PMID:33609188
Genome-wide identification and gene-editing of pigment transporter genes in the swallowtail butterfly Papilio xuthus. PMID:33596834
Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum). PMID:33478383
Expression and function of the cdgD gene, encoding a CHASE-PAS-DGC-EAL domain protein, in Azospirillum brasilense. PMID:33436847
Bioinformatic mapping of a more precise Aspergillus niger degradome. PMID:33436802
Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets. PMID:33430106
Systemic paralogy and function of retinal determination network homologs in arachnids. PMID:33225889
New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. PMID:33213521
A genome-wide screening for RNAi pathway proteins in Acari. PMID:33183236
Two Distinct Modes of Lysis Regulation in Campylobacter Fletchervirus and Firehammervirus Phages. PMID:33142851
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PMID:33125363
Presence of low virulence chytrid fungi could protect European amphibians from more deadly strains. PMID:33106491
Ascertaining the biochemical function of an essential pectin methylesterase in the gut microbe Bacteroides thetaiotaomicron. PMID:33097594
New developments in RiPP discovery, enzymology and engineering. PMID:32935693
Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade. PMID:32932820
Detecting the nature and solving the crystal structure of a contaminant protein from an opportunistic pathogen. PMID:32880586
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery. PMID:32873609
Selection and Characterization of Mutants Defective in DNA Methylation in Neurospora crassa. PMID:32873602
Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. PMID:32868406
Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). PMID:32867696
Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response. PMID:32866160
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut. PMID:32841606
Genomic Characterization and Expression Analysis of Basic Helix-Loop-Helix (bHLH) Family Genes in Traditional Chinese Herb Dendrobium officinale. PMID:32824436
A high-quality sponge gourd (Luffa cylindrica) genome. PMID:32821411
Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. PMID:32819293
Dead cells release a 'necrosignal' that activates antibiotic survival pathways in bacterial swarms. PMID:32814767
Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses. PMID:32811430
Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates. PMID:32742312
Mycobacterium tuberculosis FasR senses long fatty acyl-CoA through a tunnel and a hydrophobic transmission spine. PMID:32710080
Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer. PMID:32703190
A comprehensive survey of integron-associated genes present in metagenomes. PMID:32689930
Transcriptome Sequencing and Chemical Analysis Reveal the Formation Mechanism of White Florets in Carthamus tinctorius L. PMID:32635570
Tol-Pal System and Rgs Proteins Interact to Promote Unipolar Growth and Cell Division in Sinorhizobium meliloti. PMID:32605980
Proteomics of Galápagos Marine Iguanas Links Function of Femoral Gland Proteins to the Immune System. PMID:32581039
CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information. PMID:32580303
Roles of LysM and LytM domains in resuscitation-promoting factor (Rpf) activity and Rpf-mediated peptidoglycan cleavage and dormant spore reactivation. PMID:32434927
Genomic Identification, Evolution, and Expression Analysis of Collagen Genes Family in Water Buffalo during Lactation. PMID:32384775
Characterization of the Nitrate Transporter gene family and functional identification of HvNRT2.1 in barley (Hordeum vulgare L.). PMID:32324773
Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster. PMID:32236137
Opossum Cathelicidins Exhibit Antimicrobial Activity Against a Broad Spectrum of Pathogens Including West Nile Virus. PMID:32194564
Genome of the webworm Hyphantria cunea unveils genetic adaptations supporting its rapid invasion and spread. PMID:32183717
Genome-wide identification and expression analysis of PUB genes in cotton. PMID:32143567
Mode of Action of the Catalytic Site in the N-Terminal Ribosome-Inactivating Domain of JIP60. PMID:32123042
Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis. PMID:32050897
A Thermolabile Phospholipase B from Talaromyces marneffei GD-0079: Biochemical Characterization and Structure Dynamics Study. PMID:32033124
Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle. PMID:32024948
Reducing Aspergillus fumigatus Virulence through Targeted Dysregulation of the Conidiation Pathway. PMID:32019801
Comparative genomic analysis of selenium utilization traits in different marine environments. PMID:31993987
Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasiliense. PMID:31992632
Fam151b, the mouse homologue of C.elegans menorin gene, is essential for retinal function. PMID:31949211
Proteomic analysis reflects an environmental alkalinization-coupled pH-dependent mechanism of regulating lignocellulases in Trichoderma guizhouense NJAU4742. PMID:31938041
Widespread Dysregulation of Long Noncoding Genes Associated With Fatty Acid Metabolism, Cell Division, and Immune Response Gene Networks in Xenobiotic-exposed Rat Liver. PMID:31926019
RNA-Seq Analysis Identified XLOC_009190 as Potential Therapeutic Target for Lung Adenocarcinoma. PMID:31908488
Transcriptional Differences of Coding and Non-Coding Genes Related to the Absence of Melanocyte in Skins of Bama Pig. PMID:31905971
Analysis of MADS-box genes revealed modified flowering gene network and diurnal expression in pineapple. PMID:31896347
Analysis of EYA3 Phosphorylation by Src Kinase Identifies Residues Involved in Cell Proliferation. PMID:31847183
Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere. PMID:31831837
Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. PMID:31768035
Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean. PMID:31690594
Uncovering and characterizing splice variants associated with survival in lung cancer patients. PMID:31652257
Genome-Wide Analysis of the YABBY Gene Family in Grapevine and Functional Characterization of VvYABBY4. PMID:31649691
Prediction of protein architectures involved in the signaling-pathway initiating sporulation in Firmicutes. PMID:31647017
Genome-Wide Analysis of Dynamin Gene Family in cassava (Manihot esculenta Crantz) and Transcriptional Regulation of Family Members ARC5 in Hormonal Treatments. PMID:31615135
Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco (Nicotiana tabacum L.). PMID:31614589
Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon. PMID:31572312
Hexa-Longin domain scaffolds for inter-Rab signalling. PMID:31562761
Redox-dependent gating of VDAC by mitoNEET. PMID:31527235
A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity. PMID:31522888
MbnH is a diheme MauG-like protein associated with microbial copper homeostasis. PMID:31511324
New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea. PMID:31507553
Compartmentalized Synthesis of Triacylglycerol at the Inner Nuclear Membrane Regulates Nuclear Organization. PMID:31422915
CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. PMID:31411686
The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs. PMID:31406137
Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock. PMID:31380022
Origins of peptidases. PMID:31377195
FunFam protein families improve residue level molecular function prediction. PMID:31319797
The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley. PMID:31314154
Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass. PMID:31276273
Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton. PMID:31262248
Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion. PMID:31231410
An Aggregation-defective Mutant of Methanothermobacter sp. CaT2 Reveals Unique Protein-dependent Aggregation. PMID:31189768
Pericentrin-mediated SAS-6 recruitment promotes centriole assembly. PMID:31182187
Switching the Post-translational Modification of Translation Elongation Factor EF-P. PMID:31178848
Evolutionary analyses of NIN-like proteins in plants and their roles in nitrate signaling. PMID:31161283
The diguanylate cyclase AdrA regulates flagellar biosynthesis in Pseudomonas fluorescens F113 through SadB. PMID:31147571
Density-dependent resistance protects Legionella pneumophila from its own antimicrobial metabolite, HGA. PMID:31134893
Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. PMID:31123136
MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. PMID:31116477
A novel conserved family of Macro-like domains-putative new players in ADP-ribosylation signaling. PMID:31106069
Identification and comparative analysis of the CIPK gene family and characterization of the cold stress response in the woody plant Prunus mume. PMID:31106064
Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization. PMID:31104845
Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. PMID:31092555
Genome-wide identification, characterization, and expression patterns of the BZR transcription factor family in sugar beet (Beta vulgaris L.). PMID:31072335
A Genome-Wide Helicobacter pylori Morphology Screen Uncovers a Membrane-Spanning Helical Cell Shape Complex. PMID:31036730
Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle. PMID:30988401
Cyclin D-Cdk4,6 Drives Cell-Cycle Progression via the Retinoblastoma Protein's C-Terminal Helix. PMID:30982746
Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat. PMID:30975075
Elucidating genomic patterns and recombination events in plant cybrid mitochondria. PMID:30968307
A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy. PMID:30947258
Marine RNA Virus Quasispecies Are Distributed throughout the Oceans. PMID:30944212
Transcriptome Analysis Suggests the Roles of Long Intergenic Non-coding RNAs in the Growth Performance of Weaned Piglets. PMID:30936891
Metagenomic reconstructions of gut microbial metabolism in weanling pigs. PMID:30914068
Identification of the two-component guaiacol demethylase system from Rhodococcus rhodochrous and expression in Pseudomonas putida EM42 for guaiacol assimilation. PMID:30859469
Cell Shape and Population Migration Are Distinct Steps of Proteus mirabilis Swarming That Are Decoupled on High-Percentage Agar. PMID:30858303
Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway. PMID:30856229
Validation and Stabilization of a Prophage Lysin of Clostridium perfringens by Using Yeast Surface Display and Coevolutionary Models. PMID:30850429
Anaerobic Degradation of Sulfated Polysaccharides by Two Novel Kiritimatiellales Strains Isolated From Black Sea Sediment. PMID:30833937
Flax (Linum usitatissimum L.) response to non-optimal soil acidity and zinc deficiency. PMID:30813909
Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. PMID:30802244
First high-quality draft genome of Ochrobactrum haematophilum P6BS-III, a highly glyphosate-tolerant strain isolated from agricultural soil in Argentina. PMID:30800585
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. PMID:30768156
Whole-Genome Sequence of Multidrug-Resistant Bibersteinia trehalosi Strain OADDL-BT1. PMID:30746527
Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters. PMID:30729188
Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves. PMID:30705313
Disentangling the complexity of low complexity proteins. PMID:30698641
Identification of novel autoinducer-2 receptors in Clostridia reveals plasticity in the binding site of the LsrB receptor family. PMID:30696769
The Cdk8/19-cyclin C transcription regulator functions in genome replication through metazoan Sld7. PMID:30695077
Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). PMID:30678298
The Evolutionary Traceability of a Protein. PMID:30649284
A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. PMID:30616511
Niche-directed evolution modulates genome architecture in freshwater Planctomycetes. PMID:30610231
Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis. PMID:30608924
Functional Prediction of Hypothetical Proteins from Shigella flexneri and Validation of the Predicted Models by Using ROC Curve Analysis. PMID:30602087
Statistical investigations of protein residue direct couplings. PMID:30596639
The Tudor protein Veneno assembles the ping-pong amplification complex that produces viral piRNAs in Aedes mosquitoes. PMID:30566680
Eleven quick tips to build a usable REST API for life sciences. PMID:30543619
Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases. PMID:30541427
Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. PMID:30504906
Characterization of bHLH/HLH genes that are involved in brassinosteroid (BR) signaling in fiber development of cotton (Gossypium hirsutum). PMID:30482177
Virome analyses of Hevea brasiliensis using small RNA deep sequencing and PCR techniques reveal the presence of a potential new virus. PMID:30477549
Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria. PMID:30466434
Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria. PMID:30462661
Evolution of the Symbiosis-Specific GRAS Regulatory Network in Bryophytes. PMID:30459800
Parallel identification of novel antimicrobial peptide sequences from multiple anuran species by targeted DNA sequencing. PMID:30458708
Dissemination of Genetic Acquisition/Loss Provides a Variety of Quorum Sensing Regulatory Properties in Pseudoalteromonas. PMID:30453700
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. PMID:30407568
Kauniolide synthase is a P450 with unusual hydroxylation and cyclization-elimination activity. PMID:30405138
Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.). PMID:30400808
Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PMID:30395585
Identification and Expression Analyses of SBP-Box Genes Reveal Their Involvement in Abiotic Stress and Hormone Response in Tea Plant (Camellia sinensis). PMID:30380795
Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings. PMID:30366362
Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube. PMID:30353116
Identification of an apiosyltransferase in the plant pathogen Xanthomonas pisi. PMID:30335828
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. PMID:30289528
Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family. PMID:30283468
Protein AMPylation by an Evolutionarily Conserved Pseudokinase. PMID:30270044
Deep generative models of genetic variation capture the effects of mutations. PMID:30250057
Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments. PMID:30244836
Molecular Evolution of GDP-D-Mannose Epimerase (GME), a Key Gene in Plant Ascorbic Acid Biosynthesis. PMID:30233629
Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species. PMID:30233505
Diversity of Active Viral Infections within the Sphagnum Microbiome. PMID:30217851
Metagenomic Analysis of Fish-Associated Ca. Parilichlamydiaceae Reveals Striking Metabolic Similarities to the Terrestrial Chlamydiaceae. PMID:30202970
Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs. PMID:30189656
The CIF1 protein is a master orchestrator of trypanosome cytokinesis that recruits several cytokinesis regulators to the cytokinesis initiation site. PMID:30171070
Polygenic Analysis in Absence of Major Effector ATF1 Unveils Novel Components in Yeast Flavor Ester Biosynthesis. PMID:30154260
Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature. PMID:30152871
Genomic analysis of an Argentinean isolate of Spodoptera frugiperda granulovirus reveals that various baculoviruses code for Lef-7 proteins with three F-box domains. PMID:30133523
A singular nitric oxide synthase with a globin domain found in Synechococcus PCC 7335 mobilizes N from arginine to nitrate. PMID:30131503
Functional and Genome Sequence-Driven Characterization of tal Effector Gene Repertoires Reveals Novel Variants With Altered Specificities in Closely Related Malian Xanthomonas oryzae pv. oryzae Strains. PMID:30127769
Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. PMID:30116038
RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants. PMID:30092758
Iron-Sulfur Cluster Biosynthesis in Algae with Complex Plastids. PMID:30085124
Cysteine-mediated decyanation of vitamin B12 by the predicted membrane transporter BtuM. PMID:30072686
FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants. PMID:30071011
Systems analysis of intracellular pH vulnerabilities for cancer therapy. PMID:30065243
Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.). PMID:30061549
A Phosphatidylinositol 3-Kinase Effector Alters Phagosomal Maturation to Promote Intracellular Growth of Francisella. PMID:30057173
Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold. PMID:30057025
The Helicobacter pylori cell shape promoting protein Csd5 interacts with the cell wall, MurF, and the bacterial cytoskeleton. PMID:30039535
Endosymbiont genomes yield clues of tubeworm success. PMID:30022157
Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode. PMID:30021519
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. PMID:30016513
Early mannitol-triggered changes in the Arabidopsis leaf (phospho)proteome reveal growth regulators. PMID:30010984
Codon usage clusters correlation: towards protein solubility prediction in heterologous expression systems in E. coli. PMID:30006617
Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands. PMID:30005604
Transcriptome analysis of Cd-treated switchgrass root revealed novel transcripts and the importance of HSF/HSP network in switchgrass Cd tolerance. PMID:30003312
Centrosome Remodelling in Evolution. PMID:29986477
Transcriptomics Analysis of the Chinese Pear Pathotype of Alternaria alternata Gives Insights into Novel Mechanisms of HSAF Antifungal Activities. PMID:29932128
3DPatch: fast 3D structure visualization with residue conservation. PMID:29931189
Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. PMID:29909521
HMMER web server: 2018 update. PMID:29905871
A TALE of shrimps: Genome-wide survey of homeobox genes in 120 species from diverse crustacean taxa. PMID:29899973
Hobbit regulates intracellular trafficking to drive insulin-dependent growth during Drosophila development. PMID:29891564
A Marine Isolate of Bacillus pumilus Secretes a Pumilacidin Active against Staphylococcus aureus. PMID:29882934
Ancient Origin of the CARD-Coiled Coil/Bcl10/MALT1-Like Paracaspase Signaling Complex Indicates Unknown Critical Functions. PMID:29881386
Molecular mechanism of modulating arrestin conformation by GPCR phosphorylation. PMID:29872229
Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes. PMID:29867909
Functional Characterization of a Small Alarmone Hydrolase in Corynebacterium glutamicum. PMID:29867827
Decoding the Divergent Subcellular Location of Two Highly Similar Paralogous LEA Proteins. PMID:29857468
Comparative expression analysis identifies the respiratory transition-related miRNAs and their target genes in tissues of metamorphosing Chinese giant salamander (Andrias davidianus). PMID:29843595
A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations. PMID:29794166
Cotesia congregata Bracovirus Circles Encoding PTP and Ankyrin Genes Integrate into the DNA of Parasitized Manduca sexta Hemocytes. PMID:29769342
Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z. PMID:29764287
Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species. PMID:29752561
Dynamic Changes in Yeast Phosphatase Families Allow for Specialization in Phosphate and Thiamine Starvation. PMID:29748198
Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1. PMID:29735745
oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. PMID:29733379
Mathematical Basis of Predicting Dominant Function in Protein Sequences by a Generic HMM-ANN Algorithm. PMID:29700659
Genomic variation in 3,010 diverse accessions of Asian cultivated rice. PMID:29695866
Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades. PMID:29688542
Hypoxia enhances lignification and affects the anatomical structure in hydroponic cultivation of carrot taproot. PMID:29680943
Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T , a moderate halophilic bacterium isolated from the human gut microflora. PMID:29675845
Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes. PMID:29670199
Characterizing Phage Genomes for Therapeutic Applications. PMID:29642590
Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse. PMID:29614953
Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis. PMID:29540682
Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities. PMID:29476141
Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre. PMID:29476140
Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes. PMID:29474932
Structural properties of the linkers connecting the N- and C- terminal domains in the MocR bacterial transcriptional regulators. PMID:29450126
Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host-parasite communication. PMID:29410780
The Ancient Link between G-Protein-Coupled Receptors and C-Terminal Phospholipid Kinase Domains. PMID:29362235
Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions. PMID:29345620
Inferring joint sequence-structural determinants of protein functional specificity. PMID:29336305
Identification of a novel botulinum neurotoxin gene cluster in Enterococcus. PMID:29323697
Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice. PMID:29320982
Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici. PMID:29312156
Differential gene expression in response to Fusarium oxysporum infection in resistant and susceptible genotypes of flax (Linum usitatissimum L.). PMID:29297347
Are Fireworms Venomous? Evidence for the Convergent Evolution of Toxin Homologs in Three Species of Fireworms (Annelida, Amphinomidae). PMID:29293976
Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems. PMID:29263101
Structural, expression and evolutionary analysis of the non-specific phospholipase C gene family in Gossypium hirsutum. PMID:29258435
Inferring defense-related gene families in Arabidopsis and wheat. PMID:29258426
Genomic features of bacterial adaptation to plants. PMID:29255260
RNA degradation by the plant RNA exosome involves both phosphorolytic and hydrolytic activities. PMID:29255150
Identification, characterization, expression profiling, and virus-induced gene silencing of armadillo repeat-containing proteins in tomato suggest their involvement in tomato leaf curl New Delhi virus resistance. PMID:29250708
Diverse NADase effector families mediate interbacterial antagonism via the type VI secretion system. PMID:29237732
Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families. PMID:29222525
RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions. PMID:29220456
In Vitro Biosynthetic Studies of Bottromycin Expand the Enzymatic Capabilities of the YcaO Superfamily. PMID:29200283
Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea. PMID:29198957
A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges. PMID:29194919
Complete Genome Sequence of Bacillus velezensis L-1, Which Has Antagonistic Activity against Pear Diseases. PMID:29192072
Transcriptome and Metabolome Analyses Provide Insights into the Occurrence of Peel Roughing Disorder on Satsuma Mandarin (Citrus unshiu Marc.) Fruit. PMID:29163622
Genome-wide identification of long non-coding RNA genes and their association with insecticide resistance and metamorphosis in diamondback moth, Plutella xylostella. PMID:29158595
Severe Fertility Effects of sheepish Sperm Caused by Failure To Enter Female Sperm Storage Organs in Drosophila melanogaster. PMID:29158336
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. PMID:29145643
Resurrecting ancestral genes in bacteria to interpret ancient biosignatures. PMID:29133450
Genome Sequences of Chancellor, Mitti, and Wintermute, Three Subcluster K4 Phages Isolated Using Mycobacterium smegmatis mc2155. PMID:29122858
Genome-Wide Identification and Expression, Protein-Protein Interaction and Evolutionary Analysis of the Seed Plant-Specific BIG GRAIN and BIG GRAIN LIKE Gene Family. PMID:29118774
TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci. PMID:29106666
iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. PMID:29106644
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
Genome Analysis and Genetic Stability of the Cryptophlebia leucotreta Granulovirus (CrleGV-SA) after 15 Years of Commercial Use as a Biopesticide. PMID:29099796
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. PMID:29092050
TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules. PMID:29088312
Development of functional ectopic compound eyes in scarabaeid beetles by knockdown of orthodenticle. PMID:29078401
Prediction of protein disorder based on IUPred. PMID:29076577
Complete Genome Sequence of Alteromonas Virus vB_AspP-H4/4. PMID:29074645
Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age. PMID:29071738
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. PMID:29069476
Functional classification of protein toxins as a basis for bioinformatic screening. PMID:29066768
Proteomics analysis of Trichoplusia ni midgut epithelial cell brush border membrane vesicles. PMID:29064633
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
Chemosensing of honeybee parasite, Varroa destructor: Transcriptomic analysis. PMID:29026097
A structural model for microtubule minus-end recognition and protection by CAMSAP proteins. PMID:28991265
A uORF Represses the Transcription Factor AtHB1 in Aerial Tissues to Avoid a Deleterious Phenotype. PMID:28956754
Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations. PMID:28912564
The periplasmic transaminase PtaA of Pseudomonas fluorescens converts the glutamic acid residue at the pyoverdine fluorophore to α-ketoglutaric acid. PMID:28912270
The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition. PMID:28910638
Genome-Wide Association Study Identifies NBS-LRR-Encoding Genes Related with Anthracnose and Common Bacterial Blight in the Common Bean. PMID:28848595
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PMID:28846689
Metabolic Reconstruction and Modeling Microbial Electrosynthesis. PMID:28827682
Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase. PMID:28820334
MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. PMID:28819315
Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. PMID:28815929
The genome analysis of Oleiphilus messinensis ME102 (DSM 13489T) reveals backgrounds of its obligate alkane-devouring marine lifestyle. PMID:28802691
Ticks from diverse genera encode chemokine-inhibitory evasin proteins. PMID:28778927
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. PMID:28749930
Sequence-based identification of inositol monophosphatase-like histidinol-phosphate phosphatases (HisN) in Corynebacterium glutamicum, Actinobacteria, and beyond. PMID:28720084
A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria. PMID:28696203
1.8 Å resolution crystal structure of the carbapenem intrinsic resistance protein CarF. PMID:28695855
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. PMID:28682307
Identification of long non-coding RNA in the horse transcriptome. PMID:28676104
Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis. PMID:28675161
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. PMID:28673540
Genome-Wide Identification of AP2/ERF Transcription Factors in Cauliflower and Expression Profiling of the ERF Family under Salt and Drought Stresses. PMID:28642765
ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer. PMID:28549153
Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage. PMID:28542527
Selectivity determinants of GPCR-G-protein binding. PMID:28489817
The molecular mechanism of the type IVa pilus motors. PMID:28474682
Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1. PMID:28472331
Comparative transcriptome analysis of venom glands from Cotesia vestalis and Diadromus collaris, two endoparasitoids of the host Plutella xylostella. PMID:28465546
SeMPI: a genome-based secondary metabolite prediction and identification web server. PMID:28453782
Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biologic conflicts. PMID:28441108
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. PMID:28431173
Mroh1, a lysosomal regulator localized by WASH-generated actin. PMID:28424231
Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress. PMID:28417911
Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species. PMID:28403834
Genome-Wide Investigation of WRKY Transcription Factors Involved in Terminal Drought Stress Response in Common Bean. PMID:28386267
Genome Sequence of Mannheimia haemolytica Serotype 1 Strain 16041065 BH. PMID:28385859
Genome Sequence of a Spontaneous Nonhemolytic Mutant of Mannheimia haemolytica 16041065 GH. PMID:28385858
Characterization of the first naturally thermostable terpene synthases and development of strategies to improve thermostability in this family of enzymes. PMID:28371548
Comparative Transcriptome Reveals Benzenoid Biosynthesis Regulation as Inducer of Floral Scent in the Woody Plant Prunus mume. PMID:28344586
Identification and Expression Analysis of the Complete Family of Zebrafish pkd Genes. PMID:28271061
The Role of the Secondary Coordination Sphere in a Fungal Polysaccharide Monooxygenase. PMID:28257189
A new genome-mining tool redefines the lasso peptide biosynthetic landscape. PMID:28244986
Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. PMID:28211852
Syntrophic linkage between predatory Carpediemonas and specific prokaryotic populations. PMID:28211847
Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development. PMID:28207760
Structure of the Escherichia coli ProQ RNA-binding protein. PMID:28193673
Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. PMID:28168014
The Carboxy Terminus of YCF1 Contains a Motif Conserved throughout >500 Myr of Streptophyte Evolution. PMID:28164224
Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax. PMID:28066475
Foamy-like endogenous retroviruses are extensive and abundant in teleosts. PMID:28058112
Roles of Aquaporins in Setaria viridis Stem Development and Sugar Storage. PMID:28018372
Expansion of divergent SEA domains in cell surface proteins and nucleoporin 54. PMID:27977898
BRENDA in 2017: new perspectives and new tools in BRENDA. PMID:27924025
CATH: an expanded resource to predict protein function through structure and sequence. PMID:27899584
Early evolution of polyisoprenol biosynthesis and the origin of cell walls. PMID:27812422
Antibody-Based Therapy for Enterococcal Catheter-Associated Urinary Tract Infections. PMID:27795399
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. PMID:27789692
IMG/M: integrated genome and metagenome comparative data analysis system. PMID:27738135
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis. PMID:27729520
A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes. PMID:27718356
Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum. PMID:27695302
Data from computational analysis of the peptide linkers in the MocR bacterial transcriptional regulators. PMID:27668276
Genome-wide identification and analysis of JHBP-domain family members in the silkworm Bombyx mori. PMID:27631967
Comprehensive analysis and discovery of drought-related NAC transcription factors in common bean. PMID:27604581
Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence. PMID:27602570
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. PMID:27602057
Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress. PMID:27586959
Comprehensive analysis of SET domain gene family in foxtail millet identifies the putative role of SiSET14 in abiotic stress tolerance. PMID:27585852
Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. PMID:27578558
The Ki-67 and RepoMan mitotic phosphatases assemble via an identical, yet novel mechanism. PMID:27572260
Responses of the arcto-boreal krill species Thysanoessa inermis to variations in water temperature: coupling Hsp70 isoform expressions with metabolism. PMID:27558691
Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. PMID:27506905
Advances in the characterization of RNA-binding proteins. PMID:27503141
The multiple evolutionary origins of the eukaryotic N-glycosylation pathway. PMID:27492357
Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere. PMID:27482928
The Complete Genome Sequence of Plodia Interpunctella Granulovirus: Evidence for Horizontal Gene Transfer and Discovery of an Unusual Inhibitor-of-Apoptosis Gene. PMID:27472489
The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS. PMID:27427956
Species- and Strain-Specific Adaptation of the HSP70 Super Family in Pathogenic Trypanosomatids. PMID:27371955
WRKY transcription factor genes in wild rice Oryza nivara. PMID:27345721
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. PMID:27322404
The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. PMID:27286965
Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. PMID:27274991
Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products. PMID:27234886
ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation. PMID:27231034
An EF-hand-containing Protein in Trypanosoma brucei Regulates Cytokinesis Initiation by Maintaining the Stability of the Cytokinesis Initiation Factor CIF1. PMID:27226595
Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.). PMID:27168720
Structure, organization and evolution of ADP-ribosylation factors in rice and foxtail millet, and their expression in rice. PMID:27097755
Ca2+/H+ exchange by acidic organelles regulates cell migration in vivo. PMID:27002171
Divergent polo box domains underpin the unique kinetoplastid kinetochore. PMID:26984294
Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). PMID:26911138
Classification of proteins with shared motifs and internal repeats in the ECOD database. PMID:26833690
Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad. PMID:26794318
Mechanistic insights into c-di-GMP-dependent control of the biofilm regulator FleQ from Pseudomonas aeruginosa. PMID:26712005
The Pfam protein families database: towards a more sustainable future. PMID:26673716
Complete genome sequences of bacteriophages P12002L and P12002S, two lytic phages that infect a marine Polaribacter strain. PMID:26500718
Some of the most interesting CASP11 targets through the eyes of their authors. PMID:26473983
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. PMID:26450961
Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens. PMID:26437919
Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products. PMID:26378577 -
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
PubMed citations: 24.
24 articles citing: Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
Profile Comparer Extended: phylogeny of lytic polysaccharide monooxygenase families using profile hidden Markov model alignments. PMID:31956399
Changes in Gene Expression and Metabolite Profiles in Platanus acerifolia Leaves in Response to Feeding Damage Caused by Corythucha ciliata. PMID:31311085
Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. PMID:30904393
MultiDomainBenchmark: a multi-domain query and subject database suite. PMID:30764761
Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene. PMID:28107647
A new subfamily LIP of the major intrinsic proteins. PMID:24589353
De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. PMID:24097433
Concomitant prediction of function and fold at the domain level with GO-based profiles. PMID:23514233
Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families. PMID:22770222
Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins. PMID:22024092
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. PMID:21979275
Genome-wide analysis of the heat shock transcription factors in Populus trichocarpa and Medicago truncatula. PMID:21625849
An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. PMID:21572177
Prediction of prognostic biomarkers for interferon-based therapy to hepatitis C virus patients: a meta-analysis of the NS5A protein in subtypes 1a, 1b, and 3a. PMID:20550652
Hidden Markov Models and their Applications in Biological Sequence Analysis. PMID:20190955
Riboswitch detection using profile hidden Markov models. PMID:19814811
RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils. PMID:19465378
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution. PMID:19389731
The effectiveness of position- and composition-specific gap costs for protein similarity searches. PMID:18586708
Improving model construction of profile HMMs for remote homology detection through structural alignment. PMID:17999748
HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences. PMID:17389042
Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18. PMID:17305430
The SUPERFAMILY database in 2007: families and functions. PMID:17098927
Statistical limits to the identification of ion channel domains by sequence similarity. PMID:16735758
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genetic polymorphism
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
hidden markov model
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
homologous
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
sequence motif
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
Tags
More detailed information about this field from each metasource.
genetic polymorphism
metasource: Fairsharing.orgversion: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
hidden markov model
metasource: Fairsharing.orgversion: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
homologous
metasource: Fairsharing.orgversion: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
multiple sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
sequence motif
metasource: Fairsharing.orgversion: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: HMMER Profile File Format; HMMER Profile File Format; DOI: https://doi.org/10.25504/FAIRsharing.n3rt95; Last edited: Jan. 17, 2019, 11:16 a.m.; Last accessed: Jan 03 2022 7:13 p.m.
polymorphism hidden markov model homologous multiple sequence alignment sequence motif polypeptide region
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