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TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions
M E Dalphin1, P A Stockwell, W P Tate
1Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand. mdalphin@sanger.otago.ac.nz
Nucleic Acids Research
|December 10, 1998
Summary
TransTerm-98 is an expanded database of mRNA sequences and translational control signals, featuring over 130,000 coding sequences and UTRs from 450+ species. This resource aids in analyzing gene expression and regulatory elements.
Area of Science:
- Bioinformatics
- Molecular Biology
- Genomics
Background:
- Translational control significantly impacts gene expression.
- Databases of genetic sequences are crucial for studying these regulatory mechanisms.
- Previous versions of TransTerm provided valuable data on codon contexts.
Purpose of the Study:
- To expand and enhance the TransTerm database for improved analysis of translational control signals.
- To incorporate full coding sequences and untranslated regions (UTRs) alongside existing data.
- To provide comprehensive sequence parameters and codon usage information.
Main Methods:
- Compilation of over 130,000 non-redundant coding sequences and UTRs from more than 450 species.
- Inclusion of complete genomes from 12 prokaryotic and 1 eukaryotic organism.
- Development of a relational database with a WWW interface and a flatfile format.
Main Results:
- TransTerm-98 now includes full coding sequences and UTRs, expanding upon previous versions.
- The database contains extensive data on coding sequence length, Nc, GC3, and Codon Adaptation Index (CAI).
- Codon usage tables and start/stop codon context summaries are integrated.
Conclusions:
- TransTerm-98 offers a comprehensive resource for investigating translational control signals.
- The expanded database facilitates research across a wide range of species and genomic contexts.
- Accessible via WWW interface and flatfile, TransTerm-98 supports diverse bioinformatics analyses.