Sequence Alignment
Sequence Analysis, Protein
Software
Algorithms
Molecular Sequence Data
Amino Acid Sequence
Computational Biology
Sequence Homology, Amino Acid
Proteins
Databases, Protein
Sequence Analysis, DNA
Models, Molecular
Conserved Sequence
Internet
Base Sequence
Evolution, Molecular
User-Computer Interface
Structural Homology, Protein
Sequence Analysis
Sequence Analysis, RNA
Protein Structure, Tertiary
Sequence Homology
Computer Graphics
Protein Structure, Secondary
Markov Chains
Protein Conformation
Computer Simulation
Sequence Homology, Nucleic Acid
Genome
Binding Sites
Databases, Factual
Databases, Nucleic Acid
Models, Genetic
Models, Statistical
Information Storage and Retrieval
Pattern Recognition, Automated
Cloning, Molecular
Amino Acid Motifs
Consensus Sequence
Likelihood Functions
Reproducibility of Results
Mutagenesis, Site-Directed
INDEL Mutation
Cluster Analysis
RNA
Escherichia coli
Database Management Systems
Nucleic Acid Conformation
Bone Malalignment
Multigene Family
Models, Chemical
Mutation
Artificial Intelligence
Amino Acid Substitution
Species Specificity
Catalytic Domain
DNA
Protein Binding
Structure-Activity Relationship
Substrate Specificity
Crystallography, X-Ray
Sensitivity and Specificity
Expressed Sequence Tags
Work Simplification
Bayes Theorem
Catalysis
DNA, Complementary
RNA, Untranslated
Open Reading Frames
Entropy
Archaea
Sarcocystidae
DNA Primers
Base Pairing
Genome, Human
Data Compression
Quality Control
Chromosome Mapping
Monte Carlo Method
Data Interpretation, Statistical
Computer Communication Networks
Pan troglodytes
Tetraodontiformes
Polymerase Chain Reaction
RNA, Ribosomal
Genes, Overlapping
Enzyme Stability
Nucleotide Motifs
Amino Acids
Plant Proteins
Exons
Biological Evolution
Gene Expression Profiling
Protein Engineering
Hypermedia
Molecular Sequence Annotation
Codon
Protein Structure, Quaternary
DNA, Intergenic
High-Throughput Nucleotide Sequencing
Bacteria
Gene Library
Mathematical Computing
Automation
Systems Integration
Circular Dichroism
Neural Networks (Computer)
Membrane Proteins
Hydrogen Bonding
Introns
Evaluation Studies as Topic
HMG-Box Domains
Cattle
Eukaryotic Cells
Recombination, Genetic
Oryza sativa
RNA, Bacterial
Mammals
Nucleotides
DNA Barcoding, Taxonomic
Saccharomyces cerevisiae
Solanaceae
Peptides
Synteny
Models, Theoretical
Documentation
Mutagenesis
National Library of Medicine (U.S.)
Mutagenesis, Insertional
DNA, Ribosomal
Ligands
Carrier Proteins
Imaging, Three-Dimensional
Prokaryotic Cells
Pseudogenes
Dimerization
Surgery, Computer-Assisted
Enzymes
Models, Biological
Classification
Transcription Factors
RNA, Ribosomal, 16S
Repetitive Sequences, Nucleic Acid
Models, Structural
Thermodynamics
Peptide Fragments
Plants
Tibia
Methanococcus
Molecular Structure
RNA, Messenger
Intracellular signalling: PDK1--a kinase at the hub of things. (1/38700)
Phosphoinositide-dependent kinase 1 (PDK1) is at the hub of many signalling pathways, activating PKB and PKC isoenzymes, as well as p70 S6 kinase and perhaps PKA. PDK1 action is determined by colocalization with substrate and by target site availability, features that may enable it to operate in both resting and stimulated cells. (+info)Molecular phylogeny of the ETS gene family. (2/38700)
We have constructed a molecular phylogeny of the ETS gene family. By distance and parsimony analysis of the ETS conserved domains we show that the family containing so far 29 different genes in vertebrates can be divided into 13 groups of genes namely ETS, ER71, GABP, PEA3, ERG, ERF, ELK, DETS4, ELF, ESE, TEL, YAN, SPI. Since the three dimensional structure of the ETS domain has revealed a similarity with the winged-helix-turn-helix proteins, we used two of them (CAP and HSF) to root the tree. This allowed us to show that the family can be divided into five subfamilies: ETS, DETS4, ELF, TEL and SPI. The ETS subfamily comprises the ETS, ER71, GABP, PEA3, ERG, ERF and the ELK groups which appear more related to each other than to any other ETS family members. The fact that some members of these subfamilies were identified in early metazoans such as diploblasts and sponges suggests that the diversification of ETS family genes predates the diversification of metazoans. By the combined analysis of both the ETS and the PNT domains, which are conserved in some members of the family, we showed that the GABP group, and not the ERG group, is the one most closely related to the ETS group. We also observed that the speed of accumulation of mutations in the various genes of the family is highly variable. Noticeably, paralogous members of the ELK group exhibit strikingly different evolutionary speed suggesting that the evolutionary pressure they support is very different. (+info)Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. (3/38700)
The lysosomal cysteine proteases cathepsins S and L play crucial roles in the degradation of the invariant chain during maturation of MHC class II molecules and antigen processing. The p41 form of the invariant chain includes a fragment which specifically inhibits cathepsin L but not S. The crystal structure of the p41 fragment, a homologue of the thyroglobulin type-1 domains, has been determined at 2.0 A resolution in complex with cathepsin L. The structure of the p41 fragment demonstrates a novel fold, consisting of two subdomains, each stabilized by disulfide bridges. The first subdomain is an alpha-helix-beta-strand arrangement, whereas the second subdomain has a predominantly beta-strand arrangement. The wedge shape and three-loop arrangement of the p41 fragment bound to the active site cleft of cathepsin L are reminiscent of the inhibitory edge of cystatins, thus demonstrating the first example of convergent evolution observed in cysteine protease inhibitors. However, the different fold of the p41 fragment results in additional contacts with the top of the R-domain of the enzymes, which defines the specificity-determining S2 and S1' substrate-binding sites. This enables inhibitors based on the thyroglobulin type-1 domain fold, in contrast to the rather non-selective cystatins, to exhibit specificity for their target enzymes. (+info)A single membrane-embedded negative charge is critical for recognizing positively charged drugs by the Escherichia coli multidrug resistance protein MdfA. (4/38700)
The nature of the broad substrate specificity phenomenon, as manifested by multidrug resistance proteins, is not yet understood. In the Escherichia coli multidrug transporter, MdfA, the hydrophobicity profile and PhoA fusion analysis have so far identified only one membrane-embedded charged amino acid residue (E26). In order to determine whether this negatively charged residue may play a role in multidrug recognition, we evaluated the expression and function of MdfA constructs mutated at this position. Replacing E26 with the positively charged residue lysine abolished the multidrug resistance activity against positively charged drugs, but retained chloramphenicol efflux and resistance. In contrast, when the negative charge was preserved in a mutant with aspartate instead of E26, chloramphenicol recognition and transport were drastically inhibited; however, the mutant exhibited almost wild-type multidrug resistance activity against lipophilic cations. These results suggest that although the negative charge at position 26 is not essential for active transport, it dictates the multidrug resistance character of MdfA. We show that such a negative charge is also found in other drug resistance transporters, and its possible significance regarding multidrug resistance is discussed. (+info)Anopheles gambiae Ag-STAT, a new insect member of the STAT family, is activated in response to bacterial infection. (5/38700)
A new insect member of the STAT family of transcription factors (Ag-STAT) has been cloned from the human malaria vector Anopheles gambiae. The domain involved in DNA interaction and the SH2 domain are well conserved. Ag-STAT is most similar to Drosophila D-STAT and to vertebrate STATs 5 and 6, constituting a proposed ancient class A of the STAT family. The mRNA is expressed at all developmental stages, and the protein is present in hemocytes, pericardial cells, midgut, skeletal muscle and fat body cells. There is no evidence of transcriptional activation following bacterial challenge. However, bacterial challenge results in nuclear translocation of Ag-STAT protein in fat body cells and induction of DNA-binding activity that recognizes a STAT target site. In vitro treatment with pervanadate (vanadate and H2O2) translocates Ag-STAT to the nucleus in midgut epithelial cells. This is the first evidence of direct participation of the STAT pathway in immune responses in insects. (+info)Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers. (6/38700)
Gene expression in higher eukaryotes appears to be regulated by specific combinations of transcription factors binding to regulatory sequences. The Ets factor PU.1 and the IRF protein Pip (IRF-4) represent a pair of interacting transcription factors implicated in regulating B cell-specific gene expression. Pip is recruited to its binding site on DNA by phosphorylated PU.1. PU.1-Pip interaction is shown to be template directed and involves two distinct protein-protein interaction surfaces: (i) the ets and IRF DNA-binding domains; and (ii) the phosphorylated PEST region of PU.1 and a lysine-requiring putative alpha-helix in Pip. Thus, a coordinated set of protein-protein and protein-DNA contacts are essential for PU.1-Pip ternary complex assembly. To analyze the function of these factors in vivo, we engineered chimeric repressors containing the ets and IRF DNA-binding domains connected by a flexible POU domain linker. When stably expressed, the wild-type fused dimer strongly repressed the expression of a rearranged immunoglobulin lambda gene, thereby establishing the functional importance of PU.1-Pip complexes in B cell gene expression. Comparative analysis of the wild-type dimer with a series of mutant dimers distinguished a gene regulated by PU.1 and Pip from one regulated by PU.1 alone. This strategy should prove generally useful in analyzing the function of interacting transcription factors in vivo, and for identifying novel genes regulated by such complexes. (+info)Analysis of two cosmid clones from chromosome 4 of Drosophila melanogaster reveals two new genes amid an unusual arrangement of repeated sequences. (7/38700)
Chromosome 4 from Drosophila melanogaster has several unusual features that distinguish it from the other chromosomes. These include a diffuse appearance in salivary gland polytene chromosomes, an absence of recombination, and the variegated expression of P-element transgenes. As part of a larger project to understand these properties, we are assembling a physical map of this chromosome. Here we report the sequence of two cosmids representing approximately 5% of the polytenized region. Both cosmid clones contain numerous repeated DNA sequences, as identified by cross hybridization with labeled genomic DNA, BLAST searches, and dot matrix analysis, which are positioned between and within the transcribed sequences. The repetitive sequences include three copies of the mobile element Hoppel, one copy of the mobile element HB, and 18 DINE repeats. DINE is a novel, short repeated sequence dispersed throughout both cosmid sequences. One cosmid includes the previously described cubitus interruptus (ci) gene and two new genes: that a gene with a predicted amino acid sequence similar to ribosomal protein S3a which is consistent with the Minute(4)101 locus thought to be in the region, and a novel member of the protein family that includes plexin and met-hepatocyte growth factor receptor. The other cosmid contains only the two short 5'-most exons from the zinc-finger-homolog-2 (zfh-2) gene. This is the first extensive sequence analysis of noncoding DNA from chromosome 4. The distribution of the various repeats suggests its organization is similar to the beta-heterochromatic regions near the base of the major chromosome arms. Such a pattern may account for the diffuse banding of the polytene chromosome 4 and the variegation of many P-element transgenes on the chromosome. (+info)The mouse Aire gene: comparative genomic sequencing, gene organization, and expression. (8/38700)
Mutations in the human AIRE gene (hAIRE) result in the development of an autoimmune disease named APECED (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy; OMIM 240300). Previously, we have cloned hAIRE and shown that it codes for a putative transcription-associated factor. Here we report the cloning and characterization of Aire, the murine ortholog of hAIRE. Comparative genomic sequencing revealed that the structure of the AIRE gene is highly conserved between human and mouse. The conceptual proteins share 73% homology and feature the same typical functional domains in both species. RT-PCR analysis detected three splice variant isoforms in various mouse tissues, and interestingly one isoform was conserved in human, suggesting potential biological relevance of this product. In situ hybridization on mouse and human histological sections showed that AIRE expression pattern was mainly restricted to a few cells in the thymus, calling for a tissue-specific function of the gene product. (+info)Bone malalignment can occur in any bone of the body but is most common in the long bones of the arms and legs. There are several types of bone malalignment, including:
* Angular deformity: A deviation from the normal alignment of two bones meeting at a joint.
* Bowing or bending of a bone: A deviation from the normal straight line of a bone.
* Rotational deformity: A twisting or rotating of a bone around its long axis.
* Growth plate deformity: Abnormal growth or development of the growth plates in children and adolescents, leading to misalignment of the bones.
Bone malalignment can cause symptoms such as pain, stiffness, limited mobility, and difficulty performing daily activities. Treatment options for bone malalignment depend on the type and severity of the condition and may include:
* Bracing or casting to help align the bones
* Physical therapy to improve range of motion and strength
* Medications to manage pain and inflammation
* Surgery to correct the deformity and realign the bones.
Sequence alignment
Multiple sequence alignment
Alignment-free sequence analysis
List of sequence alignment software
MUSCLE (alignment software)
Binary Alignment Map
SH3D21
Structural alignment
C16orf90
LOC101928193
Zinc Finger Protein 800
TBC1D30
Point accepted mutation
C17orf50
ARMH3
Inferring horizontal gene transfer
C15orf39
C1orf21
C19orf44
FAM71E1
PRR16
Richard M. Durbin
C9orf25
Coiled-coil domain-containing protein 135
AMAP
TMEM229B
Fast statistical alignment
Structural alignment software
Baum-Welch algorithm
DECIPHER (software)
Bingham Road railway station
Ilocano grammar
Antiparallel (biochemistry)
Namaste Yoga
HR 4796
RISC-V
Apiales
FAM178B
Iota Draconis
Stanislaw Ulam
Interstate 19
Human sacrifice
TACC3
Multimedia information retrieval
Isha Upanishad
DSN1
Braille
HCONDELs
Dot matrix (disambiguation)
Quetrupillán
Olympic-Wallowa Lineament
Axial precession
Herbal medicine
Global Positioning System
High Efficiency Video Coding
Sean Eddy
Career
Kai Tak Airport
Geology of Dartmoor National Park
Accelerating Protein Sequence Alignment with Different Parallel Hardware Platforms | TU Delft Repositories
seqalign: Sequence Alignment
Protein Sequence Alignment View
Pfam: Sequence alignment for CL0452
self organizing algorithms for multiple sequence alignment
Pairwise Sequence Alignment BioCode | BioCodeKB - Learn Bioinformatics
Survey of the use of genetic algorithm for multiple sequence alignment
| Journal of Advanced Computer Science &...
https://es.mathworks.com/matlabcentral/answers/22369-command-of-alignment-for-general-sequences
Using Drosophila behavioral assays to characterize terebrid venom-peptide bioactivity | Scientific Reports
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. - fu mi publications
Pairwise sequence alignments - Protein Prediction 1 Summer Semester 2016 For Informaticians
Qualimap: evaluating next-generation sequencing alignment data. | Plataforma Andaluza de Medicina Computacional
Return base-by-base alignment coverage of reference sequence
in BioMap object - MATLAB
- MathWorks Nordic
LiBis: an ultrasensitive alignment augmentation for low-input bisulfite sequencing. | Brief Bioinform;22(4)2021 07 20. |...
CDD Conserved Protein Domain Family: 43A
Addgene pHCMV-AmphoEnv Sequencing Result - Sequence Analyzer
galaxy-user] Fetch sequence and alignments: extract blastz alignments - galaxy-user - lists.galaxyproject.org
Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes
Microbial enrichment and gene functional categories revealed on the walls of a spent fuel pool of a nuclear power plant | PLOS...
Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation: Developmental Cell
Third Borrelia Species in White-footed Mice - Volume 11, Number 7-July 2005 - Emerging Infectious Diseases journal - CDC
Comparative Analysis of SWIRM Domain-Containing Proteins in Plants
faircloth-lab · GitHub
Phylemon -- A suite of web tools for molecular evolution, phylogenetics and phylogenomics | HSLS
IJMS | Free Full-Text | Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Uncovering General Features of...
YRC Public Data Repository - Protein Structure Prediction - Protein Overview
Services - Bioinformatics Core Facility - Faculty of Medicine and Health Sciences - NTNU
Circovirus Hepatitis Infection in Heart-Lung Transplant Patient, France - Volume 29, Number 2-February 2023 - Emerging...
Algorithms7
- Many MSA tools and genetic alignment algorithms have parameter values either as default or optional making it difficult to select appropriate method and parameter values since the sequence is unknown. (onljbioinform.com)
- The proposed algorithms select appropriate alignment and parameter values based on sequence length, identity and alignment score, reducing time to optimize parameter values and prevent execution with default values. (onljbioinform.com)
- Due to the problem of the NP-complete class property, a number of researches use genetic algorithms (GA) to find a solution to the multiple sequence alignment. (sciencepubco.com)
- 2] Kosmas Karadimitrion and Donald H. Kraft, “Genetic Algorithms and The Multiple Sequence Alignment Problem in Biologyâ€, Proceedings of the Second Annual Molecular Biology and Biotechnology Conference, Baton Rouge, LA., February 1996. (sciencepubco.com)
- 13] Ben Othman, M.T. ; AbdelÂ- Azim, G., "Multiple sequence alignment based on genetic algorithms with new chromosomes representation", Electro-technical Conference (MELECON) , 2012 16th IEEE Mediterranean, http://dx.doi.org/10.1109/MELCON.2012.6196603 . (sciencepubco.com)
- What are the main differences in the algorithms of Global and Local alignment? (tu-muenchen.de)
- Traditionally, alignments are produced with automated algorithms and then checked and/or corrected "by eye " prior to phylogenetic inference . (bvsalud.org)
Similarity5
- Several researches were conducted to determine the level of similarity of a set of sequences. (sciencepubco.com)
- How can you define similarity between two protein sequences? (tu-muenchen.de)
- BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. (addgene.org)
- One of the viruses, EMC/2012, has been sequenced, and its sequence similarity to several bat CoVs suggested an animal origin, but a definitive bat species of origin has not yet been identified ( 3 ). (cdc.gov)
- This was confirmed by the high similarity (99.2%-100%) of their sequences with those available in GenBank. (who.int)
Nucleotide sequences1
- Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
Massively parallel1
- Kelly Oakeson] Next Generation Sequencing is a very high throughput, massively parallel method for sequencing DNA. (cdc.gov)
Bioinformatics7
- Detecting similarities between (RNA, DNA, and protein) sequences is an important part of bioinformatics. (tudelft.nl)
- 11] Naznin, F. ; Sarker , R. ; Essam, D., "DGA: Decomposition with genetic algorithm for multiple sequence alignment", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology ( CIBCB) , 2010, http://dx.doi.org/10.1109/CIBCB.2010.5510595 . (sciencepubco.com)
- Bioinformatics: sequence and genome analysis. (tu-muenchen.de)
- Sarah Gregory] Today, I'm talking with Dr. Kelly Oakeson about bioinformatics and genome sequencing in a public health lab. (cdc.gov)
- Sarah Gregory] I understand that the ability of this sequencing to work optimally is dependent on bioinformatics. (cdc.gov)
- So, bioinformatics combines computer science and biology in order to make heads or tails out of all of this sequence data we're making. (cdc.gov)
- I think a general lack of understanding as to what bioinformatics is and how important it is, especially when dealing with next generation sequence data. (cdc.gov)
Genome sequences2
- Additional genome sequences from this virus are needed to aid diagnostics, monitor population dynamics, identify the animal source, and characterize mechanisms of pathogenesis. (cdc.gov)
- Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2. (cdc.gov)
Pairwise5
- The third Alignment Reference option is Pairwise . (rcsb.org)
- When Pairwise is selected the Protein Sequence Alignment View will focus on the whole aligned section between Query and Entity sequences displaying all details of the alignment including gaps in both sequences. (rcsb.org)
- Another algorithm (SOSW) performs pairwise alignment and progressively aligns it to a local multiple sequence alignment (MSA) based on the alignment score. (onljbioinform.com)
- Write a tool that retrieves all Uniprot entries with a given EC number and calculates pairwise sequence similarities. (tu-muenchen.de)
- Compare the species horse ( Equus caballus ), Minke whale ( Balaenoptera acutorostrata ) and Red kangaroo ( Macropus rufus ) based on two of their proteins (do pairwise alignments and compare sequence identities). (tu-muenchen.de)
Protein sequences1
- alignment but designed for DNA or protein sequences. (mathworks.com)
Methods6
- Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. (bvsalud.org)
- Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods . (bvsalud.org)
- To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics . (bvsalud.org)
- Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. (pitt.edu)
- Observer agreement for event sequences: Methods and software for sequence alignment and reliability estimates. (bvsalud.org)
- Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci. (cdc.gov)
Homologous2
- 14] Kumar S, Filipski A (2007) Multiple sequence alignment: In pursuit of homologous DNA positions. (sciencepubco.com)
- The alignment of CHROMOSOMES at homologous sequences. (bvsalud.org)
Primers6
- Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
- List of commonly used primers detected in a given nucleotide sequence. (addgene.org)
- We describe a strategy for rapidly designing the primers necessary for reverse transcription and cDNA amplification of such diverse RNA viruses and report the full-genome determination of the novel CoV directly from patient sputum using next-generation short-read sequencing. (cdc.gov)
- JX869059) were analyzed to identify all possible primer-like sequences (melting temperature 58°C-60°C, guanine plus cytosine content 35%-60%) yielding 357,198 potential primers. (cdc.gov)
- Reverse complements of the 3′ mapping sequences were prepared, resulting in a set of 60 primers for the 15 amplicons (4 primers/amplicon). (cdc.gov)
- ABSTRACT A diagnostic polymerase chain reaction (PCR) assay using species-specific primers and direct sequencing was used to identify members of the Anopheles maculipennis complex in the north-west and central regions of the Islamic Republic of Iran. (who.int)
Traditionally1
- Traditionally, sequences are gastroenteritis (AGE) in humans. (cdc.gov)
Algorithm15
- A global multiple sequence alignment algorithm (SOGA) includes 2 new operators which perform a self organizing crossover and mutation operation for the required number of generations. (onljbioinform.com)
- Key Words: Algorithm, sequence alignment. (onljbioinform.com)
- Sequence Alignment by Genetic Algorithm ", Nucleic Acid Research, Vol. 24, 1515-1524, 1996 http://dx.doi.org/10.1093/nar/24.8.1515 . (sciencepubco.com)
- Batouche, M. , "Multiple sequence alignment by quantum genetic algorithm", 20th International Parallel and Distributed Processing Symposium (IPDPS), 2006, http://dx.doi.org/10.1109/IPDPS.2006.1639617 . (sciencepubco.com)
- 5] Naznin F, Sarker R, Essam D. "Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment. (sciencepubco.com)
- 6] Naznin, F. ; Sarker , R. ; Essam, D., "Progressive Alignment Method Using Genetic Algorithm for Multiple Sequence Alignment", IEEE Transactions on Evolutionary Computation, Vol 16, Issue: 5, http://dx.doi.org/10.1109/TEVC.2011.2162849 . (sciencepubco.com)
- 7] Pramanik, S. ; Setua, S.K., "A steady state Genetic Algorithm for Multiple Sequence Alignment", International Conference on Advances in Computing, Communications and Informatics (ICACCI), 2014, http://dx.doi.org/10.1109/ICACCI.2014.6968251 . (sciencepubco.com)
- 8] Liu Chao ; Liu Shuai, "The research on DNA multiple sequence alignment based on adaptive immune genetic algorithm", International Conference on Electronics and Optoelectronics (ICEOE) , 2011, Vol 3, http://dx.doi.org/10.1109/ICEOE.2011.6013304 . (sciencepubco.com)
- 12] Miranda, L.A. ; Caetano, M.A.F. ; Melo, A.C.M.A. ; Correa, J.M. ; Bordim, J.L., "Multiple Biological Sequence Alignment with a Parallel Island Injection Genetic Algorithm", 12th IEEE International Conference on High Performance Computing and Communications (HPCC) , 2010, http://dx.doi.org/10.1109/HPCC.2010.31 . (sciencepubco.com)
- Find the best alignment between the sequences "WHAT" and "WHY", using the Needleman-Wunsch algorithm, with +1 for a match, -1 for a mismatch, and -2 for a gap. (tu-muenchen.de)
- Write a small program that calculates a global alignment by implementing the Needleman-Wunsch algorithm and prints out the alignment. (tu-muenchen.de)
- Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. (clinbioinfosspa.es)
- Web-based to query sequences using a k-mer (DNA substring) based algorithm. (cdc.gov)
- BLAST algorithm against a set of reference sequences followed by notypes [6 ] with viruses in GI, GII, GVIII and GIX infecting humans. (cdc.gov)
- HuCaT uses an algorithm based on number of matching queries, k-mers are used to calculate the actual matching nucleic acid k-mers (short substrings of DNA [n 9 nt in number of nucleotide sequence matches for type assignment using the HuCaT]) to build alignments between query and reference sequences. (cdc.gov)
Viruses3
- We used high-throughput sequencing to identify viruses on tomato samples showing virus-like symptoms. (mdpi.com)
- The full HA and NA genes of 16 H1N1-positive samples obtained in our study and 21 published HA sequences and 20 published NA sequences from Jordanian viruses that were available on online gene databases were analysed. (who.int)
- Kelly Oakeson] Well, whole genome sequence data provides a very high-resolution tool for everything from identifying what types of microbes or viruses you might have in any given sample to determining antimicrobial resistance and identifying clusters of related microbes in the case of a foodborne illness outbreak. (cdc.gov)
Genomes2
- Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. (bvsalud.org)
- The large size (30,000 nt) and high variability of CoV RNA genomes present a challenge for sequencing. (cdc.gov)
Evolutionary3
- Multiple Sequence Alignment (MSA) is used in genomic analysis, such as the identification of conserved sequence motifs, the estimation of evolutionary divergence between sequences, and the genes’ historical relationships inference. (sciencepubco.com)
- Increasing the number of sequences from three to seven significantly improved the predictive value of evolutionary computations. (nih.gov)
- Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. (pitt.edu)
Biological3
- I did not mean swalign or nwalign, these just for biological sequences. (mathworks.com)
- if not are there anyone wrote a code of sequence alignment for non biological sequences in matlab? (mathworks.com)
- Kelly Oakeson] Yeah, so Next Generation Sequencing generates a lot of sequence data that need to be translated into meaningful biological information. (cdc.gov)
Subtype2
Reads1
- selects the base position with the most reads aligned to it, then uses its alignment coverage value for the bin. (mathworks.com)
Homology1
- Based on the domain architectures and the amino acid sequence homology, the SWIRM domains can be classified into three main types: Swi3/MYSM1 (human MYb-like, Swirm, and Mpn domain-containing protein-1), LSD1 (Lysine-specific demethylase 1), and Ada2 (Adenosine deaminase isoenzymes 2) types [ 13 ]. (hindawi.com)
Genotype2
- All but 1 of these isolates was relegated to the zoonotic HEV genotype 3, and the remaining sequence represented the recently discovered rat genotype from the United States and Germany. (cdc.gov)
- HBV DNA from clipper 16 clustered with genotype A sequences from SA, India, Brazil and Martinique, while clipper 20 clustered with SA genotype D sequences. (who.int)
Statistical2
- We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. (bvsalud.org)
- Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. (clinbioinfosspa.es)
Genomic3
- Venom-peptide research and drug discovery has increased exponentially with the advance of genomic-transcriptomic sequencing and proteomic mass-spectrometry 10 . (nature.com)
- RESULTS: We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. (clinbioinfosspa.es)
- A direct genomic approach was implemented in which total DNA from the sample was purified through a column-based method, followed by sequencing on the Nanopore GridION. (bvsalud.org)
Gastroenteritis1
- 4. Section III, Editing and Interpreting Entries, Guides for the determination of the probability of sequence, Interpretation of "highly improbable", deleted diarrhea and gastroenteritis of infectious origin from the list of infections that may be accepted as "due to" any other disease. (cdc.gov)
Amino1
- The computational sequence-profile analysis indicates that the typical SWIRM domain consists of 85 amino acid residues and forms a compact helix-turn-helix (HTH)-related structure [ 12 ]. (hindawi.com)
GenBank1
- The sequences were are associated with high morbidity and submitted to GenBank under accession mortality ( 1 ). (who.int)
Clipboard1
- The sequence clipboard box will appear with the top strand sequence of the selected region. (addgene.org)
Integers3
- and both integers are smaller than the length of the reference sequence. (mathworks.com)
- Column vector of nonnegative integers, each defining the start of a range in the reference sequence. (mathworks.com)
- Column vector of nonnegative integers, each defining the end of a range in the reference sequence. (mathworks.com)
Analysis1
- HA and NA sequences each in the analysis. (who.int)
Display the sequence2
- Aligned regions are represented using color code blocks that display the sequence identity through a gradient color code. (rcsb.org)
- To select a portion of sequence, click one location on the plasmid and then a second location to display the sequence between the two locations. (addgene.org)
References1
- In this case Entity sequences will be used as references. (rcsb.org)
Multiple3
- Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. (fu-berlin.de)
- It converts a multiple sequence alignment files into an HMM profile. (cdc.gov)
- Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. (cdc.gov)
Deselect1
- To deselect, click back on the nucleotide sequence. (addgene.org)
Data11
- MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. (bvsalud.org)
- However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. (bvsalud.org)
- Use with SnapGene software or the free Viewer to visualize additional data and align other sequences. (addgene.org)
- Qualimap: evaluating next-generation sequencing alignment data. (clinbioinfosspa.es)
- MOTIVATION: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. (clinbioinfosspa.es)
- Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses. (clinbioinfosspa.es)
- then only the maximum hit for all reference sequences will be grouped into primary data. (cdc.gov)
- Data from COVID-19 case investigations, contact tracing, the Commonwealth's immunization registry and whole genome sequencing were collated and analysed as part of this study. (who.int)
- Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections. (cdc.gov)
- Sarah Gregory] Ok, so what does sequence data in a public health lab do for us? (cdc.gov)
- It allows us to quickly generate huge amounts of data and DNA sequence in a very short period of time. (cdc.gov)
Provides graphical1
- The Protein Sequence Alignment View provides graphical summaries of the aligned regions when a sequence search is performed. (rcsb.org)
Next-generation1
- Sarah Gregory] And following on that, what is Next Generation Sequencing? (cdc.gov)
Conservation2
- What does "conservation" mean in the context of sequence alignments? (tu-muenchen.de)
- Despite the small p16 sequence database, our calculations of high conservation correctly predicted loss of cell cycle arrest function in 75% of tested codons, and low conservation correctly predicted wild-type function in 80-90% of codons. (nih.gov)
Mutations2
Implementation3
- A sequential implementation of Smith-Waterman requires quadratic running time with respect to the length of the sequences. (tudelft.nl)
- 10] Al Junid, S.A.M. ; Reffin, M.S. ; Majid, Z.A. ; Tahir , N.M. ; Har on, M.A., "Implementation of genetic algor ithm for optimizing DNA sequence alignment", IEEE Business Engineering and Industrial Applications Colloquium ( BEIAC) , 2012. (sciencepubco.com)
- The key reform here will be the alignment of the governing bodies' resolutions with corporate priorities, ensuring a more strategic and disciplined approach to decision-making by the Health Assembly, and enabling the necessary oversight of programme and financial implementation, including the fiscal soundness of Organizational practices. (who.int)
Results1
- A score columm then compares alignment to validate results. (onljbioinform.com)
BLAST1
- Noroviruses are associated with an compared to an established set of reference sequences to determine estimated 70,000-200,000 deaths annually [2,3 ] while sapoviruses genotypes and polymerase types based on phylogenetic clustering, or by primarily cause sporadic AGE in young children although outbreaks in employing NCBI BLAST web service. (cdc.gov)
Analyses1
- Afin de remédier à ce problème et d'étudier les variations génétiques et antigéniques des virus A(H1N1)pdm09 et H3N2, nous avons procédé à des analyses génétiques et phylogénétiques des gènes de l'hémagglutinine (HA) et de la neuraminidase (NA) de ces virus, sur la période 2011-2013 en Jordanie. (who.int)
Approaches2
- Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus , to compare different alignment approaches. (bvsalud.org)
- Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time -intensive than traditional approaches. (bvsalud.org)
Reference7
- Query sequence is used as a reference to display the aligned regions. (rcsb.org)
- The Alignment Reference drop down menu selects the reference that is used to display the aligned regions. (rcsb.org)
- By default the Query option is selected to use the Query sequence as reference. (rcsb.org)
- The Alignment Reference can be changed to Subject . (rcsb.org)
- Nonnegative integer that defines the start of a range in the reference sequence. (mathworks.com)
- Nonnegative integer that defines the end of a range in the reference sequence. (mathworks.com)
- Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. (cdc.gov)
Displays2
- The bottom track displays the aligned regions of the Entity sequence including Entity sequence gaps (or Query sequence insertions) as dashed lines or Entity sequence deletions as white circles in the middle of blocks. (rcsb.org)
- Thank you for your patience as we work to enhance our plasmid and sequence displays. (addgene.org)
View3
- The Query sequence is displayed in the first track of the Protein Sequence Alignment View. (rcsb.org)
- The first track of the Protein Sequence Alignment View will display the particular Entity sequence excluding any potential gap resulting from the alignment. (rcsb.org)
- Use text editor or plasmid mapping software to view sequence. (addgene.org)
Correspond2
- Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily- sound groups, regardless of alignment type and support threshold. (bvsalud.org)
- Content or materials that correspond with the sequence of learning experiences and help teachers and students meet learning objectives. (cdc.gov)