Sequence Alignment Concept

subject area of

• 3D-aligned tetrameric ion channels with universal residue labels for comparative structural analysis.  Journal Articles
• Molecular characterization of the Pseudomonas aeruginosa serotype O5 (PAO1) B‐band lipopolysaccharide gene cluster  Journal Articles
• d -Ala- d -Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB  Journal Articles
• A T-to-G Transversion at Nucleotide −567 Upstream of HBG2 in a GATA-1 Binding Motif Is Associated with Elevated Hemoglobin F  Journal Articles
• A dominant autoinflammatory disease caused by non-cleavable variants of RIPK1  Journal Articles
• A draft genome of Yersinia pestis from victims of the Black Death  Journal Articles
• A homology model of the pore domain of a voltage-gated calcium channel is consistent with available SCAM data  Journal Articles
• A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin  Journal Articles
• A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov.  Journal Articles
• A spliceosomal intron in Giardia lamblia  Journal Articles
• Adenosine kinase and ribokinase – the RK family of proteins  Journal Articles
• Alternative expression analysis by RNA sequencing.  Journal Articles
• An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli  Journal Articles
• An unusual myosuppressin from the blood-feeding bugRhodnius prolixus  Journal Articles
• Ancient Whole Genome Enrichment Using Baits Built from Modern DNA  Journal Articles
• Application of the Character Compatibility Approach to Generalized Molecular Sequence Data: Branching Order of the Proteobacterial Subdivisions  Journal Articles
• Architecture and Pore Block of Eukaryotic Voltage-Gated Sodium Channels in View of NavAb Bacterial Sodium Channel Structure  Journal Articles
• Association of Neurofilament Proteins with Neuronal Cdk5 Activator  Journal Articles
• Biallelic variants inWARS2encoding mitochondrial tryptophanyl-tRNA synthase in six individuals with mitochondrial encephalopathy  Journal Articles
• Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins  Journal Articles
• Biosynthetic Characterization and Chemoenzymatic Assembly of the Cryptophycins. Potent Anticancer Agents from Nostoc Cyanobionts  Journal Articles
• Case Study: Ancient Sloth DNA Recovered from Hairs Preserved in Paleofeces  Journal Articles
• Characterization and Reconstitution of Drosophila γ-Tubulin Ring Complex Subunits  Journal Articles
• Characterization of a third ras gene, rasB, that is expressed throughout the growth and development of Dictyostelium discoideum.  Journal Articles
• Characterization of non-8–17 sequences uncovers structurally diverse RNA-cleaving deoxyribozymes  Journal Articles
• Characterization of the PilN, PilO and PilP type IVa pilus subcomplex  Journal Articles
• Characterization of the Putative Type III Secretion ATPase CdsN (Cpn0707) ofChlamydophila pneumoniae  Journal Articles
• Characterization of the Shope Fibroma Virus DNA Ligase Gene  Journal Articles
• Chemical and biosynthetic evolution of the antimycin-type depsipeptides  Journal Articles
• Chemoenzymatic Synthesis of Cryptophycin/Arenastatin Natural Products  Journal Articles
• Chimeric Structure of the NAD(P)+- and NADP+-dependent Malic Enzymes ofRhizobium (Sinorhizobium) meliloti  Journal Articles
• Chitinase Genes Responsive to Cold Encode Antifreeze Proteins in Winter Cereals  Journal Articles
• Cloning and Some Novel Characteristics of Mitochondrial Hsp70 from Chinese Hamster Cells  Journal Articles
• Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum.  Journal Articles
• Cloning of HSP70 (dnaK) gene from Clostridium perfringens using a general polymerase chain reaction based approach  Journal Articles
• Cold-Active Winter Rye Glucanases with Ice-Binding Capacity  Journal Articles
• Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness  Journal Articles
• Compensatory neutral mutations and the evolution of RNA.  Journal Articles
• Complex host-pathogen coevolution in the Apterostigma fungus-growing ant-microbe symbiosis.  Journal Articles
• Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs  Journal Articles
• Conservation of Lotus and Arabidopsis Basic Helix-Loop-Helix Proteins Reveals New Players in Root Hair Development      Journal Articles
• Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria  Journal Articles
• Core Histones of the Amitochondriate Protist, Giardia lamblia  Journal Articles
• Cyclin-dependent Kinase 5 (Cdk5) Activation Domain of Neuronal Cdk5 Activator  Journal Articles
• D-TACC: a novel centrosomal protein required for normal spindle function in the early Drosophila embryo.  Journal Articles
• DATABASES OF HUMAN HEMOGLOBIN VARIANTS AND OTHER RESOURCES AT THE GLOBIN GENE SERVER  Journal Articles
• De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome  Journal Articles
• Developmental changes in the adhesive disk during Giardia differentiation  Journal Articles
• Distinct functional motifs within the IL-17 receptor regulate signal transduction and target gene expression  Journal Articles
• Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division  Journal Articles
• Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum  Journal Articles
• Diversity of T-cell receptor alpha gene transcripts in the newborn and adult periphery  Journal Articles
• Drosophila RhoGAP68F is a putative GTPase activating protein for RhoA participating in gastrulation  Journal Articles
• Dynamically Driven Ligand Selectivity in Cyclic Nucleotide Binding Domains  Journal Articles
• E-MEM: efficient computation of maximal exact matches for very large genomes  Journal Articles
• Elbow and Noc define a family of zinc finger proteins controlling morphogenesis of specific tracheal branches  Journal Articles
• Encoding of a Homolog of the IFN-γ Receptor by Myxoma Virus  Journal Articles
• Ermap, a gene coding for a novel erythroid specific adhesion/receptor membrane protein  Journal Articles
• Establishing the Principles of Recognition in the Adenine-Binding Region of an Aminoglycoside Antibiotic Kinase [APH(3‘)-IIIa]  Journal Articles
• Evidence for Dual Binding Sites for 1,1,1-Trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) in Insect Sodium Channels  Journal Articles
• Evidence for Lateral Transfer of Genes Encoding Ferredoxins, Nitroreductases, NADH Oxidase, and Alcohol Dehydrogenase 3 from Anaerobic Prokaryotes to Giardia lamblia and Entamoeba histolytica  Journal Articles
• Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis  Journal Articles
• Evolution of genes and genomes on the Drosophila phylogeny  Journal Articles
• Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: The importance of taxon-sampling in codon-based models  Journal Articles
• Evolution of the chaperonin families (HSP60, HSP 10 and TCP‐1) of proteins and the origin of eukaryotic cells  Journal Articles
• Evolutionary affinity of billfishes (Xiphiidae and Istiophoridae) and flatfishes (Plueronectiformes): Independent and trans-subordinal origins of endothermy in teleost fishes  Journal Articles
• Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta  Journal Articles
• Evolutionary and mechanistic insights into substrate and product accommodation of CTP:phosphocholine cytidylyltransferase from Plasmodium falciparum  Journal Articles
• Exploratory analysis of multiple sequence alignments using phylogenies  Journal Articles
• Fast computation of neighbor seeds  Journal Articles
• Functional analysis of genes responsible for the synthesis of the B-band O antigen of Pseudomonas aeruginosa serotype O6 lipopolysaccharide The GenBank accession number for the sequence reported in this paper is AF035937.  Journal Articles
• Functional annotation of putative aminoglycoside antibiotic modifying proteins in Mycobacterium tuberculosis H37Rv  Journal Articles
• Genetic and Molecular Analysis of GogB, a Phage-encoded Type III-secreted Substrate in Salmonella enterica Serovar Typhimurium with Autonomous Expression from its Associated Phage  Journal Articles
• Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori  Journal Articles
• HISEA: HIerarchical SEed Aligner for PacBio data  Journal Articles
• HYBRIDIZATION AND POPULATION GENETICS OF TWO MACAQUE SPECIES IN SULAWESI, INDONESIA  Journal Articles
• High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China  Journal Articles
• Homology Models of μ-Opioid Receptor with Organic and Inorganic Cations at Conserved Aspartates in the Second and Third Transmembrane Domains  Journal Articles
• Human cytomegalovirus US9 protein contains an N-terminal signal sequence and a C-terminal mitochondrial localization domain, and does not alter cellular sensitivity to apoptosis  Journal Articles
• Human homologues of Delta-1 and Delta-4 function as mitogenic regulators of primitive human hematopoietic cells  Journal Articles
• Identification of Rhizobium-specific intergenic mosaic elements within an essential two-component regulatory system of Rhizobium species  Journal Articles
• Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role  Journal Articles
• Identification of the Ice-Binding Surface on a Type III Antifreeze Protein with a “Flatness Function” Algorithm  Journal Articles
• Identification of the putative goldfish (Carassius auratus) magnesium transporter SLC41a1 and functional regulation in the gill, kidney, and intestine in response to dietary and environmental manipulations  Journal Articles
• In Vitro Generation of Human High-Density-Lipoprotein-Resistant Trypanosoma brucei brucei  Journal Articles
• In Vitro Selection of Structure‐Switching Signaling Aptamers  Journal Articles
• Insertion/Deletion-Based Approach for the Detection of Escherichia coli O157:H7 in Freshwater Environments  Journal Articles
• Integrated gene and species phylogenies from unaligned whole genome protein sequences  Journal Articles
• Interactions between flagellar and type III secretion proteins in Chlamydia pneumoniae  Journal Articles
• Interruption of cytokine networks by poxviruses: lessons from myxoma virus  Conferences
• Investigating β-Hydroxyenduracididine Formation in the Biosynthesis of the Mannopeptimycins  Journal Articles
• Kinked-Helices Model of the Nicotinic Acetylcholine Receptor Ion Channel and Its Complexes with Blockers: Simulation by the Monte Carlo Minimization Method  Journal Articles
• Lateral Transfers of Serine Hydroxymethyltransferase (glyA) and UDP-N-Acetylglucosamine Enolpyruvyl Transferase (murA) Genes from Free-living Actinobacteria to the Parasitic Chlamydiae  Journal Articles
• Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals  Journal Articles
• MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons  Journal Articles
• Mechanism and Diversity of the Erythromycin Esterase Family of Enzymes  Journal Articles
• Mechanism of aminoglycoside 3'-phosphotransferase type IIIa: His188 is not a phosphate-accepting residue  Journal Articles
• Menin: The Protein Behind the MEN1 Syndrome  Journal Articles
• Messenger RNAs for neurokinin and histamine receptor subtypes in isolated canine colonic crypts.  Journal Articles
• Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA  Journal Articles
• Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities  Journal Articles
• Mitochondrial DNA analysis of sympatric morphotypes of bottlenose dolphins (genus: Tursiops) in Chinese waters  Journal Articles
• Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA  Journal Articles
• Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis  Journal Articles
• Molecular cloning and functional expression of rabbit α2-antiplasmin  Journal Articles
• Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales , containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov.  Journal Articles
• Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations  Journal Articles
• Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates  Journal Articles
• Multiple spaced seeds for homology search  Journal Articles
• Naked but Not Hairless: The Pitfalls of Analyses of Molecular Adaptation Based on Few Genome Sequence Comparisons  Journal Articles
• Nonrandom localization of recombination events in human alpha satellite repeat unit variants: implications for higher-order structural characteristics within centromeric heterochromatin.  Journal Articles
• OGRe: a relational database for comparative analysis of mitochondrial genomes  Journal Articles
• Origin and Spread of Photosynthesis Based upon Conserved Sequence Features in Key Bacteriochlorophyll Biosynthesis Proteins  Journal Articles
• Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes  Journal Articles
• OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals  Journal Articles
• PITHIA: Protein Interaction Site Prediction Using Multiple Sequence Alignments and Attention  Journal Articles
• PROGRAM DESCRIPTION  Journal Articles
• Partial 28S rDNA Sequences and the Antiquity of Hydrothermal Vent Endemic Gastropods  Journal Articles
• Partial characterization of the genome of nine animal caliciviruses  Journal Articles
• Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters  Journal Articles
• Phylogenetic Analysis of Mycoplasmas Based on Hsp70 Sequences: Cloning of the dnaK (hsp70) Gene Region of Mycoplasma capricolum  Journal Articles
• Phylogenetic Analysis of the Cytochrome P450 3 (CYP3) Gene Family  Journal Articles
• Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species.  Journal Articles
• Phylogenetic and Functional Analysis of the Vertebrate Cytochrome P450 2 Family  Journal Articles
• Phylogenetic and functional analyses of the cytochrome P450 family 4  Journal Articles
• Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)  Journal Articles
• Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov.  Journal Articles
• Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria  Journal Articles
• Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups  Journal Articles
• Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species  Journal Articles
• Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae  Journal Articles
• Physiological and Molecular Characterization of Urea Transport by the Gills of the Lake Magadi Tilapia (Alcolapia Grahami)  Journal Articles
• Potassium, sodium, calcium and glutamate‐gated channels: pore architecture and ligand action  Journal Articles
• Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes  Journal Articles
• Protein Signatures Distinctive of Alpha Proteobacteria and Its Subgroups and a Model for α –Proteobacterial Evolution  Journal Articles
• Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades  Journal Articles
• Quorum sensing in Escherichia coli , Salmonella typhimurium , and Vibrio harveyi : A new family of genes responsible for autoinducer production  Journal Articles
• RASCAL Is a New Human Cytomegalovirus-Encoded Protein That Localizes to the Nuclear Lamina and in Cytoplasmic Vesicles at Late Times Postinfection  Journal Articles
• RNA secondary structure: physical and computational aspects  Journal Articles
• Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution  Journal Articles
• Rapid Evolution of the Sex-Determining Gene, transformer: Structural Diversity and Rate Heterogeneity Among Sibling Species of Drosophila  Journal Articles
• Regulation of NADH/CoQ Oxidoreductase: Do Phosphorylation Events Affect Activity?  Journal Articles
• Regulation of the Rapsyn Promoter by Kaiso and δ-Catenin  Journal Articles
• Resuscitation-Promoting Factors Are Cell Wall-Lytic Enzymes with Important Roles in the Germination and Growth of Streptomyces coelicolor  Journal Articles
• Rifampin phosphotransferase is an unusual antibiotic resistance kinase  Journal Articles
• SHRiMP2: Sensitive yet Practical Short Read Mapping  Journal Articles
• Scoring alignments by embedding vector similarity  Journal Articles
• Sequence analysis of bovine adenovirus type 3 early region 3 and fibre protein genes  Journal Articles
• Signature Sequences in Diverse Proteins Provide Evidence of a Close Evolutionary Relationship Between the Deinococcus-Thermus Group and Cyanobacteria  Journal Articles
• Signature proteins for the major clades of Cyanobacteria  Journal Articles
• Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales.  Journal Articles
• Significant differences in type IV pilin allele distribution among Pseudomonas aeruginosa isolates from cystic fibrosis (CF) versus non-CF patients  Conferences
• Site-directed mutagenesis and DNA sequence of pckA of Rhizobium NGR234, encoding phosphoenolpyruvate carboxykinase: gluconeogenesis and host-dependent symbiotic phenotype  Journal Articles
• SpEED: fast computation of sensitive spaced seeds  Journal Articles
• Spatial structure of the novel light-sensitive photoprotein berovin from the ctenophore Beroe abyssicola in the Ca2+-loaded apoprotein conformation state  Journal Articles
• Spectinomycin kinase from Legionella pneumophila. Characterization of substrate specificity and identification of catalytically important residues  Journal Articles
• Stability and peptide binding specificity of Btk SH2 domain: Molecular basis for X‐linked agammaglobulinemia  Journal Articles
• StoPK-1, a serine/threonine protein kinase from the glycopeptide antibiotic producer Streptomyces toyocaensis NRRL 15009, affects oxidative stress response  Journal Articles
• Structural Basis for Cyclic-Nucleotide Selectivity and cGMP-Selective Activation of PKG I  Journal Articles
• Structural Model for Phenylalkylamine Binding to L-type Calcium Channels  Journal Articles
• Structural and Functional Plasticity of Antibiotic Resistance Nucleotidylyltransferases Revealed by Molecular Characterization of Lincosamide Nucleotidylyltransferases Lnu(A) and Lnu(D)  Journal Articles
• Structural and Functional Studies of the Pseudomonas aeruginosa Minor Pilin, PilE  Journal Articles
• Surveillance technology for HIV-1 subtype C in Ethiopia: An env-based NASBA molecular beacon assay to discriminate between subcluster C and C′  Journal Articles
• Tetracycline-resistant coliforms in the effluent of the main sewage treatment plant in Hamilton, Ontario — do they have a common ancestral strain?  Journal Articles
• The bldD Gene of Streptomyces coelicolor A3(2): a Regulatory Gene Involved in Morphogenesis and Antibiotic Production  Journal Articles
• The Catenin p120^ctn Interacts with Kaiso, a Novel BTB/POZ Domain Zinc Finger Transcription Factor  Journal Articles
• The DY genes of the cattle MHC: expression and comparative analysis of an unusual class II MHC gene pair  Journal Articles
• The Evolutionary Origins of Eukaryotic Protein Disulfide Isomerase Domains: New Evidence from the Amitochondriate Protist Giardia lamblia  Journal Articles
• The Myxoma Virus M-T4 Gene Encodes a Novel RDEL-Containing Protein That Is Retained within the Endoplasmic Reticulum and Is Important for the Productive Infection of Lymphocytes  Journal Articles
• The Unc-119 Family of Neural Proteins is Functionally Conserved Between Humans,DrosophilaandC. Elegans  Journal Articles
• The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins  Journal Articles
• The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation inStreptomyces coelicolor  Journal Articles
• The complete N-terminal extension of heparin cofactor II is required for maximal effectiveness as a thrombin exosite 1 ligand  Journal Articles
• The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death  Journal Articles
• The membrane bound bacterial lipocalin Blc is a functional dimer with binding preference for lysophospholipids  Journal Articles
• The molecular basis of the expansive substrate specificity of the antibiotic resistance enzyme aminoglycoside acetyltransferase-6'-aminoglycoside phosphotransferase-2". The role of ASP-99 as an active site base important for acetyl transfer  Journal Articles
• The nucleotide sequence of the 5′-untranslated region of bovine viral diarrhoea virus: its use as a probe in rapid detection of bovine viral diarrhoea viruses and border disease viruses  Journal Articles
• The paradox of HBV evolution as revealed from a 16th century mummy  Journal Articles
• The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes  Journal Articles
• The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus- Thermus group and cyanobacteria  Journal Articles
• Three rhamnosyltransferases responsible for assembly of the A‐band D‐rhamnan polysaccharide in Pseudomonas aeruginosa: a fourth transferase, WbpL, is required for the initiation of both A‐band and B‐band lipopolysaccharide synthesis  Journal Articles
• Unmelanized Plumage Patterns in Old World Leaf Warblers Do Not Correspond to Sequence Variation at the Melanocortin-1 Receptor Locus (MC1R)  Journal Articles
• [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].  Journal Articles
• hEST2, the Putative Human Telomerase Catalytic Subunit Gene, Is Up-Regulated in Tumor Cells and during Immortalization  Journal Articles
• δβ-Thalassemia in an African-American: Identification of the deletion endpoints and PCR-Based diagnosis  Journal Articles