Sequence Alignment Concept

subject area of

• Molecular characterization of the Pseudomonas aeruginosa serotype O5 (PAO1) B-band lipopolysaccharide gene cluster  Academic Article
• d -Ala- d -Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB  Academic Article
• A T-to-G Transversion at Nucleotide −567 Upstream of HBG2 in a GATA-1 Binding Motif Is Associated with Elevated Hemoglobin F  Academic Article
• A dominant autoinflammatory disease caused by non-cleavable variants of RIPK1  Academic Article
• A draft genome of Yersinia pestis from victims of the Black Death  Academic Article
• A homology model of the pore domain of a voltage-gated calcium channel is consistent with available SCAM data  Academic Article
• A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin  Academic Article
• 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.  Academic Article
• A spliceosomal intron in Giardia lamblia  Academic Article
• Adenosine kinase and ribokinase – the RK family of proteins  Academic Article
• An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli  Academic Article
• An unusual myosuppressin from the blood-feeding bugRhodnius prolixus  Academic Article
• Ancient Whole Genome Enrichment Using Baits Built from Modern DNA  Academic Article
• Application of the Character Compatibility Approach to Generalized Molecular Sequence Data: Branching Order of the Proteobacterial Subdivisions  Academic Article
• Architecture and Pore Block of Eukaryotic Voltage-Gated Sodium Channels in View of NavAb Bacterial Sodium Channel Structure  Academic Article
• Association of Neurofilament Proteins with Neuronal Cdk5 Activator  Academic Article
• Biallelic variants inWARS2encoding mitochondrial tryptophanyl-tRNA synthase in six individuals with mitochondrial encephalopathy  Academic Article
• Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins  Academic Article
• Biosynthetic Characterization and Chemoenzymatic Assembly of the Cryptophycins. Potent Anticancer Agents from Nostoc Cyanobionts  Academic Article
• Case Study: Ancient Sloth DNA Recovered from Hairs Preserved in Paleofeces  Academic Article
• Characterization and Reconstitution of Drosophila γ-Tubulin Ring Complex Subunits  Academic Article
• Characterization of a third ras gene, rasB, that is expressed throughout the growth and development of Dictyostelium discoideum.  Academic Article
• Characterization of non-8–17 sequences uncovers structurally diverse RNA-cleaving deoxyribozymes  Academic Article
• Characterization of the PilN, PilO and PilP type IVa pilus subcomplex  Academic Article
• Characterization of the Putative Type III Secretion ATPase CdsN (Cpn0707) of Chlamydophila pneumoniae  Academic Article
• Characterization of the Shope Fibroma Virus DNA Ligase Gene  Academic Article
• Chemical and biosynthetic evolution of the antimycin-type depsipeptides  Academic Article
• Chemoenzymatic Synthesis of Cryptophycin/Arenastatin Natural Products  Academic Article
• Chimeric Structure of the NAD(P)+- and NADP+-dependent Malic Enzymes ofRhizobium (Sinorhizobium) meliloti  Academic Article
• Cloning and Some Novel Characteristics of Mitochondrial Hsp70 from Chinese Hamster Cells  Academic Article
• Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum.  Academic Article
• Cloning of HSP70 (dnaK) gene from Clostridium perfringens using a general polymerase chain reaction based approach  Academic Article
• Cold-Active Winter Rye Glucanases with Ice-Binding Capacity  Academic Article
• 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  Academic Article
• Compensatory neutral mutations and the evolution of RNA.  Academic Article
• Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs  Academic Article
• Conservation of Lotus and Arabidopsis Basic Helix-Loop-Helix Proteins Reveals New Players in Root Hair Development      Academic Article
• 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  Academic Article
• Core Histones of the Amitochondriate Protist, Giardia lamblia  Academic Article
• Cyclin-dependent Kinase 5 (Cdk5) Activation Domain of Neuronal Cdk5 Activator  Academic Article
• DATABASES OF HUMAN HEMOGLOBIN VARIANTS AND OTHER RESOURCES AT THE GLOBIN GENE SERVER  Academic Article
• De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome  Academic Article
• Developmental changes in the adhesive disk during Giardia differentiation  Academic Article
• Distinct functional motifs within the IL-17 receptor regulate signal transduction and target gene expression  Academic Article
• Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division  Academic Article
• Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum  Academic Article
• Diversity of T-cell receptor alpha gene transcripts in the newborn and adult periphery  Academic Article
• Drosophila RhoGAP68F is a putative GTPase activating protein for RhoA participating in gastrulation  Academic Article
• Dynamically Driven Ligand Selectivity in Cyclic Nucleotide Binding Domains  Academic Article
• E-MEM: efficient computation of maximal exact matches for very large genomes  Academic Article
• Elbow and Noc define a family of zinc finger proteins controlling morphogenesis of specific tracheal branches  Academic Article
• Encoding of a Homolog of the IFN-γ Receptor by Myxoma Virus  Academic Article
• Ermap, a gene coding for a novel erythroid specific adhesion/receptor membrane protein  Academic Article
• Establishing the Principles of Recognition in the Adenine-Binding Region of an Aminoglycoside Antibiotic Kinase [APH(3‘)-IIIa]  Academic Article
• Evidence for Dual Binding Sites for 1,1,1-Trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) in Insect Sodium Channels  Academic Article
• Evidence for Lateral Transfer of Genes Encoding Ferredoxins, Nitroreductases, NADH Oxidase, and Alcohol Dehydrogenase 3 from Anaerobic Prokaryotes to Giardia lamblia and Entamoeba histolytica  Academic Article
• 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  Academic Article
• Evolution of genes and genomes on the Drosophila phylogeny  Academic Article
• Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: The importance of taxon-sampling in codon-based models  Academic Article
• Evolution of the chaperonin families (HSP60, HSP 10 and TCP-1) of proteins and the origin of eukaryotic cells  Academic Article
• Evolutionary affinity of billfishes (Xiphiidae and Istiophoridae) and flatfishes (Plueronectiformes): Independent and trans-subordinal origins of endothermy in teleost fishes  Academic Article
• Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta  Academic Article
• Evolutionary and mechanistic insights into substrate and product accommodation of CTP:phosphocholine cytidylyltransferase from Plasmodium falciparum  Academic Article
• Exploratory analysis of multiple sequence alignments using phylogenies  Academic Article
• Fast computation of neighbor seeds  Academic Article
• Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae  Academic Article
• 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.  Academic Article
• Functional annotation of putative aminoglycoside antibiotic modifying proteins in Mycobacterium tuberculosis H37Rv  Academic Article
• 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  Academic Article
• Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori  Academic Article
• HISEA: HIerarchical SEed Aligner for PacBio data  Academic Article
• HYBRIDIZATION AND POPULATION GENETICS OF TWO MACAQUE SPECIES IN SULAWESI, INDONESIA  Academic Article
• High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China  Academic Article
• Homology Models of μ-Opioid Receptor with Organic and Inorganic Cations at Conserved Aspartates in the Second and Third Transmembrane Domains  Academic Article
• 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  Academic Article
• Human homologues of Delta-1 and Delta-4 function as mitogenic regulators of primitive human hematopoietic cells  Academic Article
• Identification of Rhizobium-specific intergenic mosaic elements within an essential two-component regulatory system of Rhizobium species  Academic Article
• 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  Academic Article
• 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  Academic Article
• In Vitro Generation of Human High-Density-Lipoprotein-Resistant Trypanosoma brucei brucei  Academic Article
• In Vitro Selection of Structure‐Switching Signaling Aptamers  Academic Article
• Insertion/Deletion-Based Approach for the Detection of Escherichia coli O157:H7 in Freshwater Environments  Academic Article
• Integrated gene and species phylogenies from unaligned whole genome protein sequences  Academic Article
• Interactions between flagellar and type III secretion proteins in Chlamydia pneumoniae  Academic Article
• Interruption of cytokine networks by poxviruses: lessons from myxoma virus  Conference Paper
• Investigating β-Hydroxyenduracididine Formation in the Biosynthesis of the Mannopeptimycins  Academic Article
• Kinked-Helices Model of the Nicotinic Acetylcholine Receptor Ion Channel and Its Complexes with Blockers: Simulation by the Monte Carlo Minimization Method  Academic Article
• Lateral Transfers of Serine Hydroxymethyltransferase (glyA) and UDP-N-Acetylglucosamine Enolpyruvyl Transferase (murA) Genes from Free-living Actinobacteria to the Parasitic Chlamydiae  Academic Article
• Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals  Academic Article
• MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons  Academic Article
• Mechanism and Diversity of the Erythromycin Esterase Family of Enzymes  Academic Article
• Mechanism of aminoglycoside 3'-phosphotransferase type IIIa: His188 is not a phosphate-accepting residue  Academic Article
• Menin: The Protein Behind the MEN1 Syndrome  Academic Article
• Messenger RNAs for neurokinin and histamine receptor subtypes in isolated canine colonic crypts.  Academic Article
• Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA  Academic Article
• Mitochondrial DNA analysis of sympatric morphotypes of bottlenose dolphins (genus: Tursiops) in Chinese waters  Academic Article
• Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA  Academic Article
• Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis  Academic Article
• Molecular cloning and functional expression of rabbit α2-antiplasmin  Academic Article
• 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.  Academic Article
• 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  Academic Article
• Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates  Academic Article
• Multiple spaced seeds for homology search  Academic Article
• Naked but Not Hairless: The Pitfalls of Analyses of Molecular Adaptation Based on Few Genome Sequence Comparisons  Academic Article
• Nonrandom localization of recombination events in human alpha satellite repeat unit variants: implications for higher-order structural characteristics within centromeric heterochromatin.  Academic Article
• OGRe: a relational database for comparative analysis of mitochondrial genomes  Academic Article
• Origin and Spread of Photosynthesis Based upon Conserved Sequence Features in Key Bacteriochlorophyll Biosynthesis Proteins  Academic Article
• Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes  Academic Article
• OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals  Academic Article
• PITHIA: Protein Interaction Site Prediction Using Multiple Sequence Alignments and Attention  Academic Article
• PROGRAM DESCRIPTION  Academic Article
• Partial 28S rDNA Sequences and the Antiquity of Hydrothermal Vent Endemic Gastropods  Academic Article
• Partial characterization of the genome of nine animal caliciviruses  Academic Article
• Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters  Academic Article
• Phylogenetic Analysis of Mycoplasmas Based on Hsp70 Sequences: Cloning of the dnaK (hsp70) Gene Region of Mycoplasma capricolum  Academic Article
• Phylogenetic Analysis of the Cytochrome P450 3 (CYP3) Gene Family  Academic Article
• Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species.  Academic Article
• Phylogenetic and Functional Analysis of the Vertebrate Cytochrome P450 2 Family  Academic Article
• Phylogenetic and functional analyses of the cytochrome P450 family 4  Academic Article
• Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)  Academic Article
• Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov.  Academic Article
• Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria  Academic Article
• Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups  Academic Article
• Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species  Academic Article
• Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae  Academic Article
• Physiological and Molecular Characterization of Urea Transport by the Gills of the Lake Magadi Tilapia (Alcolapia Grahami)  Academic Article
• Potassium, sodium, calcium and glutamate-gated channels: pore architecture and ligand action  Academic Article
• Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes  Academic Article
• Protein Signatures Distinctive of Alpha Proteobacteria and Its Subgroups and a Model for α –Proteobacterial Evolution  Academic Article
• Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades  Academic Article
• Quorum sensing in Escherichia coli , Salmonella typhimurium , and Vibrio harveyi : A new family of genes responsible for autoinducer production  Academic Article
• RASCAL Is a New Human Cytomegalovirus-Encoded Protein That Localizes to the Nuclear Lamina and in Cytoplasmic Vesicles at Late Times Postinfection  Academic Article
• RNA secondary structure: physical and computational aspects  Academic Article
• Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution  Academic Article
• Rapid Evolution of the Sex-Determining Gene, transformer: Structural Diversity and Rate Heterogeneity Among Sibling Species of Drosophila  Academic Article
• Regulation of NADH/CoQ Oxidoreductase: Do Phosphorylation Events Affect Activity?  Academic Article
• Regulation of the Rapsyn Promoter by Kaiso and δ-Catenin  Academic Article
• Resuscitation-Promoting Factors Are Cell Wall-Lytic Enzymes with Important Roles in the Germination and Growth of Streptomyces coelicolor  Academic Article
• Rifampin phosphotransferase is an unusual antibiotic resistance kinase  Academic Article
• SHRiMP2: Sensitive yet Practical Short Read Mapping  Academic Article
• Sequence analysis of bovine adenovirus type 3 early region 3 and fibre protein genes  Academic Article
• Signature Sequences in Diverse Proteins Provide Evidence of a Close Evolutionary Relationship Between the Deinococcus-Thermus Group and Cyanobacteria  Academic Article
• Signature proteins for the major clades of Cyanobacteria  Academic Article
• Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales.  Academic Article
• Significant differences in type IV pilin allele distribution among Pseudomonas aeruginosa isolates from cystic fibrosis (CF) versus non-CF patients  Conference Paper
• Site-directed mutagenesis and DNA sequence of pckA of Rhizobium NGR234, encoding phosphoenolpyruvate carboxykinase: gluconeogenesis and host-dependent symbiotic phenotype  Academic Article
• SpEED: fast computation of sensitive spaced seeds  Academic Article
• Spatial structure of the novel light-sensitive photoprotein berovin from the ctenophore Beroe abyssicola in the Ca2+-loaded apoprotein conformation state  Academic Article
• Species Specificity of Amidine-Based Urokinase Inhibitors  Academic Article
• Spectinomycin kinase from Legionella pneumophila. Characterization of substrate specificity and identification of catalytically important residues  Academic Article
• Stability and peptide binding specificity of Btk SH2 domain: Molecular basis for X-linked agammaglobulinemia  Academic Article
• StoPK-1, a serine/threonine protein kinase from the glycopeptide antibiotic producer Streptomyces toyocaensis NRRL 15009, affects oxidative stress response  Academic Article
• Structural Basis for Cyclic-Nucleotide Selectivity and cGMP-Selective Activation of PKG I  Academic Article
• Structural Model for Phenylalkylamine Binding to L-type Calcium Channels  Academic Article
• Structural and Functional Plasticity of Antibiotic Resistance Nucleotidylyltransferases Revealed by Molecular Characterization of Lincosamide Nucleotidylyltransferases Lnu(A) and Lnu(D)  Academic Article
• Structural and Functional Studies of the Pseudomonas aeruginosa Minor Pilin, PilE  Academic Article
• Structure and Activity of the Metal-independent Fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae  Academic Article
• Tetracycline-resistant coliforms in the effluent of the main sewage treatment plant in Hamilton, Ontario — do they have a common ancestral strain?  Academic Article
• The bldD Gene of Streptomyces coelicolor A3(2): a Regulatory Gene Involved in Morphogenesis and Antibiotic Production  Academic Article
• The Catenin p120^ctn Interacts with Kaiso, a Novel BTB/POZ Domain Zinc Finger Transcription Factor  Academic Article
• The DY genes of the cattle MHC: expression and comparative analysis of an unusual class II MHC gene pair  Academic Article
• The Evolutionary Origins of Eukaryotic Protein Disulfide Isomerase Domains: New Evidence from the Amitochondriate Protist Giardia lamblia  Academic Article
• 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  Academic Article
• The Unc-119 Family of Neural Proteins is Functionally Conserved Between Humans,DrosophilaandC. Elegans  Academic Article
• The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins  Academic Article
• The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation inStreptomyces coelicolor  Academic Article
• The complete N-terminal extension of heparin cofactor II is required for maximal effectiveness as a thrombin exosite 1 ligand  Academic Article
• The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death  Academic Article
• The membrane bound bacterial lipocalin Blc is a functional dimer with binding preference for lysophospholipids  Academic Article
• 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  Academic Article
• 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  Academic Article
• The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances  Academic Article
• The paradox of HBV evolution as revealed from a 16th century mummy  Academic Article
• The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes  Academic Article
• The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus- Thermus group and cyanobacteria  Academic Article
• 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  Academic Article
• Unmelanized Plumage Patterns in Old World Leaf Warblers Do Not Correspond to Sequence Variation at the Melanocortin-1 Receptor Locus (MC1R)  Academic Article
• [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].  Academic Article
• hEST2, the Putative Human Telomerase Catalytic Subunit Gene, Is Up-Regulated in Tumor Cells and during Immortalization  Academic Article
• δβ-Thalassemia in an African-American: Identification of the deletion endpoints and PCR-Based diagnosis  Academic Article