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IBM microcomputer programs that analyze DNA sequences for tRNA genes
R D Shortridge1, I L Pirtle, R M Pirtle
1Department of Biochemistry, North Texas State University/Texas College of Osteopathic Medicine, Denton 76203.
Computer Applications in the Biosciences : CABIOS
|April 1, 1986
Summary
Four computer programs identify transfer RNA (tRNA) genes in DNA sequences, predicting their cloverleaf structures. These tools aid molecular biologists in gene analysis and structure-function studies, simplifying tRNA gene identification within DNA fragments.
Area of Science:
- Bioinformatics
- Molecular Biology
- Genomics
Background:
- Transfer RNA (tRNA) genes are crucial for protein synthesis.
- Identifying tRNA genes within large DNA sequences can be challenging.
- Existing methods for tRNA gene identification may require extensive laboratory work.
Purpose of the Study:
- To develop and present a computational toolset for automated tRNA gene identification.
- To enable the prediction of tRNA secondary structures in various organisms.
- To facilitate the search for eukaryotic RNA polymerase III termination sites.
Main Methods:
- Development of four computer programs in IBM (Microsoft) BASIC.
- Implementation of algorithms to search DNA sequence data files.
- Inclusion of functions to predict secondary structures and identify termination signals.
Main Results:
- The programs successfully locate and plot predicted secondary structures of tRNA genes.
- Applicability demonstrated for eukaryotic, prokaryotic, and mitochondrial tRNA genes, including those with intervening sequences.
- Two programs can identify potential eukaryotic RNA polymerase III termination sites downstream of tRNA genes.
Conclusions:
- This software set provides an efficient method for identifying tRNA genes and their structures.
- It simplifies the process for molecular biologists, reducing the need for extensive restriction mapping.
- The tools support research in gene structure-function relationships and genomic analysis.