---
_id: '861'
abstract:
- lang: eng
text: '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.'
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.
author:
- first_name: Konstantin
full_name: Popadin, Konstantin Yu
last_name: Popadin
- first_name: Leila
full_name: Mamirova, Leila A
last_name: Mamirova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 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
apa: Popadin, K., Mamirova, L., & Kondrashov, F. (2007). A manually curated
database of tetrapod mitochondrially encoded tRNA sequences and secondary structures.
BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-8-441
chicago: Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually
Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary
Structures.” BMC Bioinformatics. BioMed Central, 2007. https://doi.org/10.1186/1471-2105-8-441.
ieee: K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of
tetrapod mitochondrially encoded tRNA sequences and secondary structures,” BMC
Bioinformatics, vol. 8. BioMed Central, 2007.
ista: Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of
tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC
Bioinformatics. 8.
mla: 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.
short: K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).
date_created: 2018-12-11T11:48:54Z
date_published: 2007-11-14T00:00:00Z
date_updated: 2021-01-12T08:20:18Z
day: '14'
doi: 10.1186/1471-2105-8-441
extern: 1
intvolume: ' 8'
month: '11'
publication: BMC Bioinformatics
publication_status: published
publisher: BioMed Central
publist_id: '6789'
quality_controlled: 0
status: public
title: A manually curated database of tetrapod mitochondrially encoded tRNA sequences
and secondary structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 8
year: '2007'
...