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Annotating Animal Mitochondrial tRNAs: A new Scoring Scheme and an Empirical Evaluation of Four Methods.

DE2004833700

Publication Date	2004
Personal Author	Wyman, S. K.; Boore, J. L.
Page Count	14
Abstract	Identification of transfer RNAs in animal mitochondrial genomes is important for many areas of genome analysis including phylogenetic reconstruction, understanding inheritance of disease, and identifying forensic materials. Animal mitochondrial tRNAs differ from the canonical tRNAs in both their secondary structure and level of conservation of nucleotide sequence and therefore, conventional tRNA or general RNA searching software cannot be used for identification and custom methods are required. Here we present the results of an experimental analysis of four different methods tested on a large dataset consisting of 5,720 tRNAs extracted from the entire set of complete animal mitochondrial genomes in GenBank. Methods were evaluated based on number of false negatives and false positives. Additionally, we present a new scoring scheme customized for animal mitochondrial tRNAs.
Keywords	Transfer RNA Animals Data sets RNA Genomes Identification Animal mitochondrial genomes
Source Agency	Technical Information Center Oak Ridge Tennessee
Corporate Authors	Texas Univ. at Austin. Dept. of Computer Sciences.; Department of Energy, Washington, DC.; DOE Joint Genome Inst., Walnut Creek, CA.
Supplemental Notes	Prepared in cooperation with DOE Joint Genome Inst., Walnut Creek, CA. Sponsored by Department of Energy, Washington, DC.
Document Type	Technical Report
NTIS Issue Number	200515

Annotating Animal Mitochondrial tRNAs: A new Scoring Scheme and an Empirical Evaluation of Four Methods.

Annotating Animal Mitochondrial tRNAs: A new Scoring Scheme and an Empirical Evaluation of Four Methods.
DE2004833700

Publication Date	2004
Personal Author	Wyman, S. K.; Boore, J. L.
Page Count	14
Abstract	Identification of transfer RNAs in animal mitochondrial genomes is important for many areas of genome analysis including phylogenetic reconstruction, understanding inheritance of disease, and identifying forensic materials. Animal mitochondrial tRNAs differ from the canonical tRNAs in both their secondary structure and level of conservation of nucleotide sequence and therefore, conventional tRNA or general RNA searching software cannot be used for identification and custom methods are required. Here we present the results of an experimental analysis of four different methods tested on a large dataset consisting of 5,720 tRNAs extracted from the entire set of complete animal mitochondrial genomes in GenBank. Methods were evaluated based on number of false negatives and false positives. Additionally, we present a new scoring scheme customized for animal mitochondrial tRNAs.
Keywords	Transfer RNA Animals Data sets RNA Genomes Identification Animal mitochondrial genomes
Source Agency	Technical Information Center Oak Ridge Tennessee
Corporate Authors	Texas Univ. at Austin. Dept. of Computer Sciences.; Department of Energy, Washington, DC.; DOE Joint Genome Inst., Walnut Creek, CA.
Supplemental Notes	Prepared in cooperation with DOE Joint Genome Inst., Walnut Creek, CA. Sponsored by Department of Energy, Washington, DC.
Document Type	Technical Report
NTIS Issue Number	200515