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tRNA
Motivation
Motivation
tRNAscan-SE
Combines these three methods
Motivation Methods Results
Phase 1 (Filtering)
Stage 1 Overview
Motivation Methods Results
Phase 1 (Filtering)
tRNAscan1.3
Phase 1 (Filtering)
tRNAscan1.3
Phase 1 (Filtering)
tRNAscan1.3
Test Breakdown:
Detection of invariant and semi-invariant bases with consensus
matrices
Detection of potential base-pairing structures
Detection of the appropriate length and position of potential
intro sequences
Motivation Methods Results
Phase 1 (Filtering)
Pavesi’s Algorithm
Searches subsequences
Detects A and B boxes (degenerate, so use weight matrix
analysis)
Transcription termination signal
Considers the spacing between these
Motivation Methods Results
Phase 1 (Filtering)
Pavesi, 1249
Motivation Methods Results
Phase 1 (Filtering)
Phase 1
Phase 1 (Filtering)
Phase 1
Runs EufindtRNA
Implementation of Pavesi’s algorithm
Motivation Methods Results
Phase 1 (Filtering)
Phase 1
Runs EufindtRNA
Implementation of Pavesi’s algorithm
Results
Combined sensitivity exceeds 99%
False positive rate is about five times tRNAscans
Motivation Methods Results
Phase 2 Overview
Motivation Methods Results
Motivation
tRNA
Context-Free Grammars
S → aSa|bSb|aa|bb
Motivation Methods Results
Context-Free Grammars
S → aSa|bSb|aa|bb
Example of a palindrome
S =⇒ aSa
=⇒ aaSaa
=⇒ aabbaa
So aabbaa is a palindrome!
Motivation Methods Results
Figure: Stem-loop
Sakurambo. (27 May 2006), stem-loop structure in RNA. Retrieved 6 April, 2011, from Wikipedia, the Free
Encyclopedia http://en.wikipedia.org/wiki/File:Stem-loop.svg
Motivation Methods Results
Context-Free Grammar
Motivation
Exceptions to the rules get left out
Motivation Methods Results
Motivation
Exceptions to the rules get left out
Adding them to the grammar degrades the pattern
Motivation Methods Results
Motivation
Exceptions to the rules get left out
Adding them to the grammar degrades the pattern
Introduce probabilities
Motivation Methods Results
Motivation
Exceptions to the rules get left out
Adding them to the grammar degrades the pattern
Introduce probabilities
Implementation
Use CYK algorithm (a parsing algorithm)
Motivation Methods Results
Covariance Model
Phase 3 Overview
Motivation Methods Results
Phase 3
Pseudogenes/false positives
Results
Motivation Methods Results
Usage
http://lowelab.ucsc.edu/cgi-bin/tRNAscan-SE.cgi
Motivation Methods Results
Usage
http://lowelab.ucsc.edu/cgi-bin/tRNAscan-SE.cgi
Motivation Methods Results
Usage
Usage
Problems
Lowe, Todd M., and Sean R. Eddy. “tRNAscan-SE: a program for improved detection of transfer RNA
genes in genomic sequence.” Nucleic Acid Research. 25.5 (1997): 955-964. Print
Pavesi, Angelo, Franco Conterio, Angelo Bolchi, Giorgio Dieci, and Simone Ottonello. “Identification of
new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of
transcriptional control regions.” Nucleic Acids Research. 22.7 (1994): 1247-1256. Print.
Eddy, Sean R., and Richard Durbin. “RNA sequence analysis using covariance models.” Nucleic Acids
Fichant, Gwennaele A., and Christian Burks. “Identifying Potential tRNA Genes in Genomic DNA
Durbin, R., S. Eddy, A. Krogh, G. Mitchison. Biological sequence analysis. Cambridge: Cambridge