Transcript Media:tRNAs - Genomics and Bioinformatics @ Davidson

Puneet Lakhmani
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Methods
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Results
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Where to go next
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tRNA scan-SE
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ARAGORN
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tRNA finder
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tRNADB-CE
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BLAST
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Count using word
Sequence
Arabidopsis Theria
Oryza sativa Japonica
Group
454
561
168
Illumina
424
131
Total
985
299
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569 tRNAs in the strawberry genome; tRNA
scan-SE scores
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600 tRNAs in the grape genome (median size
73; 43% GC content) based on thei
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454 and Illumina data overlap
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tRNA scan-SE
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Vaccinum tRNA
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Laslett, D. & Canback, B. (2004) ARAGORN, a program to detect tRNA
genes and tmRNA genes in nucleotide sequences. Nucleic Acids
Res. 32;11-16.
Lowe, T.M. and Eddy, S.R. (1997) Nucleic Acids Res, 25: 955-964.
Takashi Abe, Toshimichi Ikemura, Junichi Sugahara, Akio Kanai, Yasuo
Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko
Yamada, Akira Muto and Hachiro Inokuchi "tRNADB-CE 2011: tRNA gene
database curated manually by experts“ Nucleic Acids Research,
39(Database isuue), D210-D213, 2011.
http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/index.cgi
http://lowelab.ucsc.edu/tRNAscan-SE/
http://www.wiley.com/college/boyer/0470003790/structure/tRNA/trna_in
tro.htm