A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures

K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).

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Abstract
Background: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description: We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.
Publishing Year
Date Published
2007-11-14
Journal Title
BMC Bioinformatics
Acknowledgement
KYuP and LAM were supported by the Molecular and Cellular Biology Program of the Russian Academy of Science. KYuP was supported by the Russian Fund of Basic Research (grant 04-04-49623). LAM was partially supported by grants from the Howard Hughes Medical Institute (55005610), INTAS (05-1000008-8028). FAK is a National Science Foundation Graduate Research Fellow.
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8
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Popadin K, Mamirova L, Kondrashov F. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 2007;8. doi:10.1186/1471-2105-8-441
Popadin, K., Mamirova, L., & Kondrashov, F. (2007). A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics, 8. https://doi.org/10.1186/1471-2105-8-441
Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics 8 (2007). https://doi.org/10.1186/1471-2105-8-441.
K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures,” BMC Bioinformatics, vol. 8, 2007.
Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 8.
Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics, vol. 8, BioMed Central, 2007, doi:10.1186/1471-2105-8-441.

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