• Students from participating colleges and universities isolate and characterize bacteriophages from local environments, annotate the phage genomes, and submit the annotated sequences to the National Center for Biotechnology Information GenBank database. (hhmi.org)
  • In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. (nih.gov)
  • This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. (nih.gov)
  • THE sequencing of whole genomes of species from all kingdoms of life progresses at an ever increasing pace. (genetics.org)
  • To determine the genetic basis for chemotype-specific differences in toxin production, the genomes of four Stachybotrys strains were sequenced and assembled de novo. (nih.gov)
  • . The genomes of these four strains were obtained by massive parallel sequencing on an Illumina Hiseq 2000. (nih.gov)
  • The i5k, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community. (slideshare.net)
  • To account for the great diversity of domain contexts and an unexpected paucity of ortholog conservation, we must categorize the coding regions of completely sequenced genomes into domain families, as well as protein families. (biomedcentral.com)
  • Software for the automatic annotation of eukaryotic genomes. (biomedcentral.com)
  • Artemis is especially useful in analysing the compact genomes of bacteria, archaea and lower eukaryotes, and will cope with sequences of any size from small genes to whole genomes. (semanticscholar.org)
  • As the number of sequenced bacterial genomes rapidly expands, there is increased interest in learning how many and which of the annotated open reading frames (ORFs) fall into the category "essential. (asm.org)
  • Structures can be downloaded and displayed from the PubChem, PDB, and NCBI structure databases together with the sequences for proteins and nucleic acids. (rcsb.org)
  • We detected 1384 proteins from 327,906 peptide sequence identifications at 72 and 120 hpf with false identification rates of less than 1% using 2D LC-ESI-MS/MS. These included only ∼30% of proteins that were identified by 2D PAGE-MALDI-TOF/TOF. (mcponline.org)
  • Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS-based shotgun proteomics profiling technologies have been applied to characterize abundant proteins and metabolites, resulting in the detection of 1069 proteins and 159 metabolites. (genetics.org)
  • By integrating genomic annotation information with experimentally identified metabolites and proteins, we constructed a draft metabolic network for Chlamydomonas. (genetics.org)
  • Despite its many limitations and problems, whole-genome annotation has become a standardized data flow and initial sets of all encoded proteins can be generated in a computer-assisted and automated way. (genetics.org)
  • Our targets are mainly selected from the complete set of soluble Mycoplasma proteins and their prokaryotic homologs that have no significant sequence similarity to proteins of known structure. (strgen.org)
  • A protein band at 42 kDa was in-gel digested with Lys-N. Relatively straightforward sequencing resulted in the de novo identification of the two ostrich proteins creatine kinase and actin. (mcponline.org)
  • Under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. (wikipedia.org)
  • RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. (ncbs.res.in)
  • RNA strands are created using DNA strands as a template in a process called transcription , where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U). Under the genetic code , these RNA strands specify the sequence of amino acids within proteins in a process called translation . (wikipedia.org)
  • the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. (nih.gov)
  • Recent application of molecular genetic tools for the exploration of the metabolism of Desulfovibrio vulgaris Hildenborough has provided several new datasets that might provide insights and constraints to the electron flow pathways. (frontiersin.org)
  • The annotation of biochemical pathways resulted in a total of 11,971 unigenes assigned with 145 KEGG maps and 1759 enzyme codes. (frontiersin.org)
  • developed an algorithm to nominate biologically important fusion mutations by integrating various molecular interactions, pathways, and functional annotations [ 9 ]. (hindawi.com)
  • Together with high‐throughput biochemical characterization of dmDis3l2 and bacterial RN ase R, our results imply a conserved molecular function of RN ase II /R enzymes as "readers" of destabilizing posttranscriptional marks-uridylation in eukaryotes and adenylation in prokaryotes-that play important roles in RNA surveillance. (embopress.org)
  • Our transcriptome analysis provides insight into the fundamental role of the circadian clock in SD induction in this important model insect species, and contributes to the in-depth elucidation of the molecular regulation mechanism of insect diapause induction. (g3journal.org)
  • However, little work has been performed to elucidate the molecular basis of diapause induction in this species. (g3journal.org)
  • The primary goal of the Molecular Core is to characterize the diversity and prevalence of NTM species affecting the CF community, and to accurately identify and limit potential instances of patient-to-patient transmission or nosocomial acquisition events in CF Centers. (nationaljewish.org)
  • 1990. Chloroplast DNA sequence from a Miocene Magnolia species. (grisda.org)
  • This DNA was sequenced and compared with an extant species of Magnolia , and some other close relatives. (grisda.org)
  • This paper reports ribosomal RNA (5S rRNA) sequences from three species of green algae. (grisda.org)
  • Similarities in ribosomal RNA sequence were investigated for 15 species of amphibians, 4 species of reptiles, and 2 species of birds. (grisda.org)
  • These were compared with published sequences for one species of amphibian and four species of mammals. (grisda.org)
  • The strains include two species, S. chlorohalonata (IBT strain 40285) and S. chartarum (IBT strains 40288, 40293, and 7711), which are distinguishable both by morphology and molecular markers. (nih.gov)
  • For cDNA libraries from different species it makes sense to run a full tblastx sequence comparison of all against all. (awi.de)
  • Soybean has one of the most dense molecular maps of any crop species. (usda.gov)
  • Furthermore, genomic sequences around markers of interest found in microarray experiments can be easily retrieved and, for example, used for promoter/transcription factor analysis. (columbia.edu)
  • Our research involves a number of quantitative techniques, including database design, systematic datamining and machine learning, visualization of high-dimensional data, and molecular simulation. (yale.edu)
  • Molecule World for iPhone can be used on the iPhone or iPod touch to display and manipulate 3D chemical and molecular structures from the PubChem, PDB, or NCBI structure databases. (rcsb.org)
  • Our sequence editing software is also integrated with NCBI databases, making it easy to access and search online databases. (dnastar.com)
  • Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metage-nomics projects. (psu.edu)
  • Sequencing workflows require library quantification and normalization to ensure data quality and reduce cost. (genomeweb.com)
  • Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. (gu.se)
  • ANTHEDNA is a package of integrated UNIX freeware tools for retrieving and analyzing sequence data. (bioinformatics.org)
  • It is called ANTHEDNA because it was developed for analyzing the DNA sequence data obtained from the ribosomal database project. (bioinformatics.org)
  • We have carried out this effort by processing next-generation sequencing data (i.e. (yale.edu)
  • All data sets are made available as supplementary material as well as web-accessible databases and within the functional context via the Chlamydomonas-adapted MapMan annotation platform. (genetics.org)
  • This talk will illustrate few Hybrid Approaches used for assembling data from multiple sequencing platforms to form Hybrid Genome which allows one to correct for the biases and errors of one platform with information from a complementary platform. (selectbiosciences.com)
  • Its molecular structure was first identified by James Watson and Francis Crick at the Cavendish Laboratory within the University of Cambridge in 1953, whose model-building efforts were guided by X-ray diffraction data acquired by Raymond Gosling, who was a post-graduate student of Rosalind Franklin. (wikipedia.org)
  • Uniquely positioned within this shifting healthcare paradigm are molecular and clinical laboratories that can provide healthcare teams with access to a rich repository of actionable genetic data. (darkdaily.com)
  • Understanding that NGS services represent a major financial commitment by laboratories, the advantages of using NGS testing as a tool to retain and grow a lab's customer base is also examined, as is the importance of purchasing a best-of-breed molecular LIS created with big data, genome annotation and interpretation, and informed decision-making in mind. (darkdaily.com)
  • We also provide data management support, i.e. for publication of sequence data and data products to standard data repositories. (awi.de)
  • The USDA public databases, SoyBase and The Soybean Breeders Toolbox, provide access to map-based and sequence-based data, as well as germplasm information. (usda.gov)
  • In 2016, the Association for Molecular Pathology (AMP), in partnership with the College of American Pathologists (CAP) and American College of Molecular Genetics (ACMG), launched a set of guidelines meant to set industry standards for reporting of molecular diagnostic test results in oncology, using a tier-based system and defined levels of evidence. (genomeweb.com)
  • The zebrafish ( Danio rerio ) is an attractive vertebrate model organism for studies into the molecular mechanisms of development ( 2 ), pathology ( 3 ), and pharmacology ( 4 , 5 ). (mcponline.org)
  • The job will involve a diverse skill set which will set up an early career researcher interested in pursuing a career in molecular genetics and pathology. (niab.com)
  • First, we are interested in annotating the raw human genome sequence, especially in characterizing the vast intergenic regions. (yale.edu)
  • Delivery of the human genome draft sequence by publicly funded [ 1 ] and corporate [ 2 ] projects promises to precipitate significant biomedical advances this century. (biomedcentral.com)
  • After scientists revealed the map of the entire human genome in 2001, the ENCyclopedia Of DNA Elements (ENCODE) project was launched in September 2003 with the aim of identifying all the functional elements in the human genome sequence. (scitizen.com)
  • The results of the pilot phase which focused on 1% of the human genome sequence are published this week in Nature (today on Nature online). (scitizen.com)
  • MARRVEL : Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. (ohsu.edu)
  • In co-operation with Hochschule Bremerhaven and others, students are able to work in the field of sequence analyses participating in scientific projects at AWI. (awi.de)
  • This study aimed to test a newly devised cost-effective multiplex PCR assay for the molecular diagnosis of autosomal dominant retinitis pigmentosa (adRP), as well as the use of whole-exome sequencing (WES) to detect disease-causing mutations in adRP. (molvis.org)
  • Whole-exome sequencing was performed on 56 samples from 16 families with diverse IRD phenotypes that had remained undiagnosed after screening for known mutations using genotyping-based microarrays (Asper Ophthalmics). (arvojournals.org)
  • p>Manual validated information which has been generated by the UniProtKB automatic annotation system. (uniprot.org)
  • Despite increasing knowledge of diapause preparation, initiation, maintenance, and termination, molecular mechanisms regulating the more "upstream" stage of diapause induction remain largely unexplored. (g3journal.org)
  • Despite extensive research devoted to the hydrophobic effect, its molecular mechanisms remain controversial, and there are still no reliably predictive models for its role in protein-ligand binding. (rcsb.org)
  • Molecular Mechanisms and Structural Features of Cardiomyopathy-Causing Troponin T Mutants in the Tropomyosin Overlap Region. (ncbs.res.in)
  • SeqBuilder Pro supports virtually any type of sequence file, including FASTA, ABI, and GenBank formats, and easily imports files from Vector NTI , SnapGene, and Geneious. (dnastar.com)
  • The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. (springer.com)
  • The primary audience for this volume are molecular biologists working either in biotechnology companies or academic research environments, individual researchers and the institutions they work for, and students. (elsevier.com)
  • X-ray crystallography and molecular dynamics simulations are compatible with the proposal that the differences in binding between the homologous ligands stem from changes in the number and organization of water molecules localized in the active site in the bound complexes, rather than (or perhaps in addition to) release of structured water from the apposed hydrophobic surfaces. (rcsb.org)
  • Investigating the effect of key mutations on the conformational dynamics of toll‐like receptor dimers through molecular dynamics simulations and protein structure networks. (ncbs.res.in)
  • The authors cite other literature supporting this result, involving the amino acid sequences of beta-hemoglobin and myoglobin. (grisda.org)