• Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins . (ucsc.edu)
  • The method also revealed the structure and function of many biological molecules, including vitamins , drugs, proteins and nucleic acids such as DNA . (wikipedia.org)
  • BriX is a database containing some protein fragments from 4 to 14 residue from non-homologous proteins. (wikipedia.org)
  • UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. (blogspot.com)
  • GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. (unt.edu)
  • In this paper, in hope of recruiting database researchers into this rapidly progressing biology and medical research area, we introduce several challenges in genome informatics from the viewpoint of using existing DBMS for processing next-generation sequencer data. (springer.com)
  • Nucleic Acids Research. (wikipedia.org)
  • LRG sequences are suggested by the community studying a locus (for example, Locus-Specific Database curators, research laboratories, mutation consortia). (ucsc.edu)
  • Nucleic Acids Research 37 (Database Issue) D810-D815. (h-invitational.jp)
  • The BioToolKit, a searchable and browsable database of 400 internet research applications, includes up-to-date links to nucleic acid, genome, and protein databases, online applications for data retrieval and data analysis, and tools for molecular visualization. (bio.net)
  • Dear Sirs, I submitted the following one page paper to Nucleic Acids Research, which starting with January 1992, created a new journal where papers regarding human DNA polymorphisms are going to be published. (bio.net)
  • and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. (standardsingenomics.org)
  • The most recent Nucleic Acids Research (NAR) database special issue states that there are now over 1200 published biological databases in the accompanying online Database Collection [ 2 ]. (standardsingenomics.org)
  • A public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. (unt.edu)
  • For publication lists, we refer to the [email protected] database. (wur.nl)
  • Nucleic Acids Research 32 (2004): D377-D382. (ualberta.ca)
  • The nucleic acids and ligands database (NALD) is concerned with the identification of ligands (drugs) that bind nucleic acids (NA) and provide users with sets of specific information in relation to the binding existing between both molecules. (springer.com)
  • WO 2008156172-A/39: Double-stranded nucleic acid molecules suitable for prevention or treatment of uterine cancer, breast cancer, or bladder cancer, Agent for inhibiting cancer cell proliferation, and Medicine. (nig.ac.jp)
  • p>An evidence describes the source of an annotation, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc. (uniprot.org)
  • This can lead to a transitive annotation problem because there may be several such annotation transfers by sequence similarity between a particular database record and actual wet lab experimental information. (wikipedia.org)
  • Therefore, care must be taken when interpreting the annotation data from sequence databases. (wikipedia.org)
  • Transcriptome annotation compared known contigs from various genomic databases UniprotKB/Swissprot to the O. lurida transcriptome v3 using BLASTn and BLASTx algorithms, which resulted in a range of 164-35,687 matched contigs. (google.com)
  • This resource describes project scope, material, and objectives and provides a mechanism to retrieve datasets that are often difficult to find due to inconsistent annotation, multiple independent submissions, and the varied nature of diverse data types which are often stored in different databases. (unt.edu)
  • A collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. (unt.edu)
  • RefSeq HGMD (subset) - Subset of RefSeq Curated, transcripts annotated by the Human Gene Mutation Database. (ucsc.edu)
  • 2009) VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. (h-invitational.jp)
  • NALD thus annotates nucleic acids in complexes with ligands in terms of detailed binding interactions, binding motifs where binding occurs, binding properties, binding modes & classes and links to diseases may be in association with the ligands. (springer.com)
  • NALD provides online access to these types of information while it focuses on ligands that bind nucleic acids with implications on diseases of high prevalence in Africa and in particular in Algeria and the Southern African Development Community (SADC) region such as HIV/AIDS, cancer, hepatitis, malaria and tuberculosis. (springer.com)
  • Rachedi A., Madida K. (2013) NALD: Nucleic Acids and Ligands Database. (springer.com)
  • The K D values of CB1 ligands in the ChEMBL database are predicted by QSAR random forest (RF) modeling for the CB1 receptor and known off-targets (TRPV1, mGlu5, 5-HT1a). (springer.com)
  • Specifically, as stated by the original NIAID scope, the primary purpose of the project is to design, develop, populate and maintain a publicly accessible, comprehensive immune epitope database containing linear and conformational antibody epitopes and T-cell epitopes composed of MHC-binding peptides and ligands with a priority for epitopes associated with NIAID category AC potential bioterrorism pathogens and their toxins. (fairsharing.org)
  • An aminoacyl-tRNA synthetase ( aaRS or ARS ), also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its tRNA . (wikipedia.org)
  • It does so by catalyzing the esterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA . (wikipedia.org)
  • In humans, the 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code . (wikipedia.org)
  • This is sometimes called "charging" or "loading" the tRNA with the amino acid. (wikipedia.org)
  • Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing peptide , according to the genetic code. (wikipedia.org)
  • The synthetase first binds ATP and the corresponding amino acid (or its precursor) to form an aminoacyl-adenylate, releasing inorganic pyrophosphate (PP i ). (wikipedia.org)
  • The adenylate-aaRS complex then binds the appropriate tRNA molecule's D arm , and the amino acid is transferred from the aa-AMP to either the 2'- or the 3'-OH of the last tRNA nucleotide (A76) at the 3'-end. (wikipedia.org)
  • This can happen when two amino acids have different properties even if they have similar shapes-as is the case with Valine and Threonine . (wikipedia.org)
  • Although not all synthetases have a domain with the sole purpose of editing, they make up for it by having specific binding and activation of their affiliated amino acids. (wikipedia.org)
  • The amino acids are attached to the hydroxyl (-OH) group of the adenosine via the carboxyl (-COOH) group. (wikipedia.org)
  • In a typical scenario, an aaRS consists of a catalytic domain (where both the above reactions take place) and an anticodon binding domain (which interacts mostly with the anticodon region of the tRNA and ensures binding of the correct tRNA to the amino acid). (wikipedia.org)
  • Aligning your amino acid sequence with nucleotide sequence database by translating database sequences taking into account all six possible open reading frames. (nig.ac.jp)
  • Aligning your amino acid sequence with amino acid seque nce database. (nig.ac.jp)
  • Info about the GenBank Nucleic acid database. (bio.net)
  • GenBank consists of several divisions, most of which can be accessed through the Nucleotide database. (unt.edu)
  • REFERENCE 1 (bases 1 to 4646332) AUTHORS Mori,H., Hirai,A., Morooka,N. and Horiuchi,T. TITLE Direct Submission JOURNAL Submitted (22-AUG-2005) to the DDBJ/EMBL/GenBank databases. (nig.ac.jp)
  • Submitted (30-NOV-2008) to the DDBJ/EMBL/GenBank databases. (nig.ac.jp)
  • Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. (standardsingenomics.org)
  • Existing DBMS, whose major targets are business applications, is not suited to managing these biological data because storing such large data to DBMS is time-consuming, and also current database queries cannot accommodate various types of bioinformatics tools written in various programming languages. (springer.com)
  • In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. (wikipedia.org)
  • Searching the Nucleotide Database will yield available results from each of its component databases. (unt.edu)
  • The database offers data integration in the form of links to the PDB, DrugBank, and other resources such as UniProt and PubMed databases. (springer.com)
  • The UniProt database is an example of a protein sequence database. (wikipedia.org)
  • PolySearch 2.0 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and HMDB to improve its accuracy and coverage. (ualberta.ca)
  • Aligning your nucleotide sequence with nucleotide sequence database. (nig.ac.jp)
  • The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. (unt.edu)
  • Computer applications to biological databases. (bio.net)
  • RefSeq gene is a subset of NCBI's RefSeq database, and are defined based on review from curators of locus-specific databases and the genetic testing community. (unt.edu)
  • The RefSeq collection is accessed through the Nucleotide and Protein databases. (unt.edu)
  • In press, Nucleic Acids Res] Yeats C, Lees J, Carter P, Sillitoe I, Orengo C "The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. (ebi.ac.uk)
  • The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. (fairsharing.org)
  • EcoCyc is a model organism database for Escherichia coli K-12 MG1655. (fairsharing.org)
  • 3, 137-155 (1996) REFERENCE 9 AUTHORS Fujita,N., Mori,H., Yura,T. and Ishihama,A. TITLE Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region JOURNAL Nucleic Acids Res. (nig.ac.jp)
  • 1 BLASTN 2.2.25 [Feb-01-2011] 2 3 Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 4 Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 5 "Gapped BLAST and PSI-BLAST: a new generation of protein database search 6 programs", Nucleic Acids Res. (nig.ac.jp)
  • PolySearch 2.0 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. (ualberta.ca)
  • Database of related DNA sequences that originate from comparative studies: phylogenetic, population, environmental and, to a lesser degree, mutational. (unt.edu)
  • A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. (blogspot.com)
  • Select the target database. (nig.ac.jp)
  • CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. (uniprot.org)
  • Records in sequence databases are deposited from a wide range of sources, from individual researchers to large genome sequencing centers. (wikipedia.org)
  • The new journal, called 'Human Molecular Genetics' requires an accession number from the EMBL database. (bio.net)
  • Each record in the database is a set of DNA sequences. (unt.edu)
  • The entire database or entries within the database may be copied and redistributed freely, without advance permission, provided that its textual content is not modified. (bio.net)
  • The BioSample database contains descriptions of biological source materials used in experimental assays. (unt.edu)
  • The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access. (wur.nl)