Literature DB >> 9399869

The translational signal database, TransTerm, is now a relational database.

M E Dalphin1, C M Brown, P A Stockwell, W P Tate.   

Abstract

TransTerm-97 contains more than 97 500 non-redundant coding-sequence initiation and termination contexts compiled from GenBank, release 101 (15-June-1997). In addition, several coding sequence parameters are available: coding sequence length, Nc, GC3, and, when it is computable, codon adaptation index (CAI). Codon usage tables and summaries of start and stop codon contexts are also included. The information covers more than 325 species and organelles, including seven complete bacterial genomes and one complete eukaryotic genome. To promote research in translational control of protein synthesis, TransTerm has been converted into a relational database to ease the process of making queries. The relational database manager, Postgresql, gives access to the database using SQL (Structured Query Language). A World Wide Web interface using forms is being completed to allow the casual user access to the database. Extensions are planned to include the full 5'-UTR, full coding sequence and 3'-UTR. TransTerm-97 is available on the World Wide Web at:http://biochem. otago.ac.nz:800/Transterm/homepage.html

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Year:  1998        PMID: 9399869      PMCID: PMC147192          DOI: 10.1093/nar/26.1.335

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  5 in total

1.  The 'effective number of codons' used in a gene.

Authors:  F Wright
Journal:  Gene       Date:  1990-03-01       Impact factor: 3.688

2.  The translational signal database, TransTerm: more organisms, complete genomes.

Authors:  M E Dalphin; C M Brown; P A Stockwell; W P Tate
Journal:  Nucleic Acids Res       Date:  1997-01-01       Impact factor: 16.971

3.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

Authors:  P M Sharp; W H Li
Journal:  Nucleic Acids Res       Date:  1987-02-11       Impact factor: 16.971

4.  The translational termination signal database (TransTerm) now also includes initiation contexts.

Authors:  C M Brown; P A Stockwell; M E Dalphin; W P Tate
Journal:  Nucleic Acids Res       Date:  1994-09       Impact factor: 16.971

5.  The translational termination signal database.

Authors:  C M Brown; M E Dalphin; P A Stockwell; W P Tate
Journal:  Nucleic Acids Res       Date:  1993-07-01       Impact factor: 16.971

  5 in total
  6 in total

1.  Combinatorial codons: a computer program to approximate amino acid probabilities with biased nucleotide usage.

Authors:  E Wolf; P S Kim
Journal:  Protein Sci       Date:  1999-03       Impact factor: 6.725

2.  Indirect regulation of translational termination efficiency at highly expressed genes and recoding sites by the factor recycling function of Escherichia coli release factor RF3.

Authors:  D J Crawford; K Ito; Y Nakamura; W P Tate
Journal:  EMBO J       Date:  1999-02-01       Impact factor: 11.598

3.  Regulation of eukaryotic protein synthesis: selective influenza viral mRNA translation is mediated by the cellular RNA-binding protein GRSF-1.

Authors:  Y W Park; J Wilusz; M G Katze
Journal:  Proc Natl Acad Sci U S A       Date:  1999-06-08       Impact factor: 11.205

4.  XML-based approaches for the integration of heterogeneous bio-molecular data.

Authors:  Marco Mesiti; Ernesto Jiménez-Ruiz; Ismael Sanz; Rafael Berlanga-Llavori; Paolo Perlasca; Giorgio Valentini; David Manset
Journal:  BMC Bioinformatics       Date:  2009-10-15       Impact factor: 3.169

5.  Engineered transfer RNAs for suppression of premature termination codons.

Authors:  John D Lueck; Jae Seok Yoon; Alfredo Perales-Puchalt; Adam L Mackey; Daniel T Infield; Mark A Behlke; Marshall R Pope; David B Weiner; William R Skach; Paul B McCray; Christopher A Ahern
Journal:  Nat Commun       Date:  2019-02-18       Impact factor: 14.919

6.  Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus.

Authors:  Kati Seidl; Susanne Müller; Patrice François; Carsten Kriebitzsch; Jacques Schrenzel; Susanne Engelmann; Markus Bischoff; Brigitte Berger-Bächi
Journal:  BMC Microbiol       Date:  2009-05-18       Impact factor: 3.605

  6 in total

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