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Transterm--extended search facilities and improved integration with other databases
Grant H Jacobs1, Peter A Stockwell, Warren P Tate
1Department of Biochemistry and Centre for Gene Research, University of Otago, PO Box 56, Dunedin, New Zealand.
Nucleic Acids Research
|December 31, 2005
Summary
Transterm is an updated database providing key mRNA regions and motifs for translational control research. It now includes enhanced search capabilities and expanded data, aiding molecular biology investigations.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Transterm is a long-standing public database for mRNA sequence analysis.
- Previous versions were described in 2002, necessitating an update to reflect current data and functionalities.
Purpose of the Study:
- To describe the updated Transterm database, highlighting new features and expanded content.
- To provide researchers with enhanced tools for investigating mRNA motifs and sequences relevant to translational control.
Main Methods:
- Computationally derived data from GenBank and RefSeq for key mRNA regions (3'/5' flanking, initiation/termination signals, coding sequences).
- Incorporation of over 40 curated motifs and structural patterns important for translational control, including data from UTRsite and Rfam.
- Implementation of advanced search functionalities, including BLAST and regular expression searches, alongside user-defined pattern analysis.
Main Results:
- The database is non-redundant, allowing for species-specific summary files and statistics.
- Includes data for key mRNA regions and a curated collection of over 40 translational control motifs.
- Enhanced search options (BLAST, regular expressions) and inclusion of RefSeq data improve usability and scope.
Conclusions:
- The updated Transterm database offers a comprehensive resource for studying mRNA sequences and motifs.
- Enhanced search tools and expanded data facilitate deeper investigation into translational regulatory elements.
- Transterm continues to be a valuable tool for researchers in molecular biology and bioinformatics.