17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there...
Transcript of 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there...
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17 ½ Weeks in Leipzig, Saxonia
Andreas Gruber
Institute for Theoretical ChemistryUniversity of Vienna
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 3: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/3.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 4: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/4.jpg)
Bacterial Self Killing System
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 6: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/6.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 7: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/7.jpg)
Shigella sonnei Ss046 8Serratia proteamaculans 568 5Escherichia coli IAI1 1Enterobacter sp. 638 1Salmonella enterica 2Edwardsiella ictaluri 93-146 1Shigella boydii CDC 3083-94 10Escherichia fergusonii ATCC 35469 4Escherichia coli O157:H7 str. EC4115 16Photobacterium profundum SS9 1Proteus mirabilis HI4320 1Klebsiella pneumoniae 342 2Escherichia coli str. K-12 substr 5Photorhabdus luminescens 3Shigella flexneri 2a str. 2457T 8Shigella flexneri 2a str. 301 6Shigella boydii Sb227 6Klebsiella pneumoniae NTUH-K2044 2Vibrio fischeri ES114 1Salmonella enterica 1Cronobacter sakazakii ATCC BAA-894 6Vibrio vulnificus CMCP6 1Aliivibrio salmonicida LFI1238 3Klebsiella pneumoniae 2Shigella dysenteriae Sd197 5Shewanella baltica OS223 2Aeromonas salmonicida 2
So far ...
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 9: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/9.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 10: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/10.jpg)
functional ncRNAs
ncRNA detection with RNAz
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functional ncRNAs
structured ncRNAs
ncRNA detection with RNAz
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functional ncRNAs
structured ncRNAs
ncRNA detection with RNAz
Why focus on structured RNAs?
Structured RNAs are the only class offunctional RNAs that give at least somestatistically relevant signals.
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functional ncRNAs
structured ncRNAs
ncRNA detection with RNAz
Why focus on structured RNAs?
Structured RNAs are the only class offunctional RNAs that give at least somestatistically relevant signals.
Thermodynamic stability
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functional ncRNAs
structured ncRNAs
ncRNA detection with RNAz
Why focus on structured RNAs?
Structured RNAs are the only class offunctional RNAs that give at least somestatistically relevant signals.
Thermodynamic stability
Structural conservation
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 16: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/16.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 17: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/17.jpg)
Thermodynamic stability
z-score = E - μ
Background
σBackground
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Thermodynamic stability
z-score = E - μ
Background
σBackground
1) Generate randomized sequences of the same length and same base composition
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Thermodynamic stability
z-score = E - μ
Background
σBackground
1) Generate randomized sequences of the same length and same base composition
2) Fold the sequences using RNAfold
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Thermodynamic stability
z-score = E - μ
Background
σBackground
1) Generate randomized sequences of the same length and same base composition
2) Fold the sequences using RNAfold
3) calculate μ and σ
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 22: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/22.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 23: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/23.jpg)
The Wash way
Explicit generation and folding of sequences is too costly!
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The Wash way
Explicit generation and folding of sequences is too costly!
Clue: Regression - train a SVM instead that does the job!
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The Wash way
Explicit generation and folding of sequences is too costly!
Clue: Regression - train a SVM instead that does the job!
for length (50 ... 400 by 50) { for C+G (0.25 ... 0.75 by 0.05) { for A/(A+U) (0.25 ... 0.75 by 0.05) { for C/(C+G) (0.25 ... 0.75 by 0.05) { 1) generate a synthetic sequence of given length with nucleotide frequencies derived from C+G, A/(A+U), and C/(C+G)
2) generate 1,000 shuffled sequences 3) fold those 1,000 sequences and calculate μ and σ } } }}
==> ~ 10,000 training examples to train a SVM for μ and σ, respectively.
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The Wash way
Explicit generation and folding of sequences is too costly!
Clue: Regression - train a SVM instead that does the job!
for length (50 ... 400 by 50) { for C+G (0.25 ... 0.75 by 0.05) { for A/(A+U) (0.25 ... 0.75 by 0.05) { for C/(C+G) (0.25 ... 0.75 by 0.05) { 1) generate a synthetic sequence of given length with nucleotide frequencies derived from C+G, A/(A+U), and C/(C+G)
2) generate 1,000 shuffled sequences 3) fold those 1,000 sequences and calculate μ and σ } } }}
==> ~ 10,000 training examples to train a SVM for μ and σ, respectively.
Energy minimization is based on stacking energies!
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The Wash way
Explicit generation and folding of sequences is too costly!
Clue: Regression - train a SVM instead that does the job!
for length (50 ... 400 by 50) { for C+G (0.25 ... 0.75 by 0.05) { for A/(A+U) (0.25 ... 0.75 by 0.05) { for C/(C+G) (0.25 ... 0.75 by 0.05) { 1) generate a synthetic sequence of given length with nucleotide frequencies derived from C+G, A/(A+U), and C/(C+G)
2) generate 1,000 shuffled sequences 3) fold those 1,000 sequences and calculate μ and σ } } }}
==> ~ 10,000 training examples to train a SVM for μ and σ, respectively.
Energy minimization is based on stacking energies!
It would be better to consider dinucleotide composition as well!
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 29: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/29.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 30: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/30.jpg)
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Generate Sequences
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Generate Sequences
Shuffle
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Generate Sequences
Shuffle
Vary LengthRepresentative Set
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Generate Sequences
Shuffle
Vary LengthRepresentative Set
μ, σ
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Generate Sequences
Shuffle
Vary LengthRepresentative Set
μ, σSplit to Subsets
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Generate Sequences
Shuffle
Vary LengthRepresentative Set
μ, σSplit to Subsets
Train
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 38: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/38.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 39: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/39.jpg)
NEW
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NEW
NEW
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NEW
NEWNEW
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 43: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/43.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 44: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/44.jpg)
We did it!
![Page 45: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/45.jpg)
We did it!
![Page 46: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/46.jpg)
We did it!
![Page 47: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/47.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 48: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/48.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 49: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/49.jpg)
Structural vs. sequence based alignments
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 51: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/51.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 52: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/52.jpg)
On a genome wide scale
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Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 54: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/54.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 55: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/55.jpg)
Manja agruber||||| ||||| ||||| |||| ||||| ||||| ||||| ||||||| ||||| ||||| ||||||
Dom agruber||||| ||||| ||||| ||||| ||||| ||||| ||||| ||||||| |||||
![Page 56: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/56.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 57: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/57.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 58: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/58.jpg)
J. Mattick
![Page 59: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/59.jpg)
Alu repeats
J. Mattick
![Page 60: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/60.jpg)
Alu repeats
J. Mattick
Retrotransposition
![Page 61: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/61.jpg)
Alu repeats
J. Mattick
Retrotransposition
Pseudogenes
![Page 62: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/62.jpg)
Alu repeats
J. Mattick
Retrotransposition
Pseudogenes
Expressed Sequence Tags (ESTs)
![Page 63: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/63.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 64: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/64.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 65: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/65.jpg)
BLAST query: > 75% query coverage, > 95% identity
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BLAST query: > 75% query coverage, > 95% identity
?
![Page 67: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/67.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 68: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/68.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 69: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/69.jpg)
![Page 70: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/70.jpg)
Full length match
![Page 71: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/71.jpg)
Partial match
Full length match
![Page 72: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/72.jpg)
77% of ESTs with U1 snRNA sigantures are Chimeras
Partial match
Full length match
Chimera
![Page 73: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/73.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 74: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/74.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 75: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/75.jpg)
What do we learn?
Chimera are most likely artifacts caused during the process of library generation.
There are expressed RNA pseudogenes.
Small ncRNAs can be found in ESTs but it is likely that they are fused to something else.
In most cases only the protein component is annotated.
![Page 76: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/76.jpg)
What's the plan?
There are lots of ESTs and there are lots of sequenced genomes!
A pipeline for detection of chimeric ESTs and hence expressed small ncRNAs is in production.
What do we learn?
Chimera are most likely artifacts caused during the process of library generation.
There are expressed RNA pseudogenes.
Small ncRNAs can be found in ESTs but it is likely that they are fused to something else.
In most cases only the protein component is annotated.
![Page 77: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/77.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 78: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/78.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 79: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/79.jpg)
Some C. elegans snoRNAs have a tRNA-like promoter
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Some C. elegans snoRNAs have a tRNA-like promoter
Is there a already powerfulbox-A-box-B-finder?
![Page 81: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/81.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 82: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/82.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 83: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/83.jpg)
Yes, there is!
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.Nucleic Acids Res. (1997) 25(5)
tRNAscan-SE
![Page 84: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/84.jpg)
Yes, there is!
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.Nucleic Acids Res. (1997) 25(5)
tRNAscan-SE
tRNAscan algorithm
* screen for putative box A and box b motifs
* then call the computationally more costly structure validation
![Page 85: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/85.jpg)
Yes, there is!
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.Nucleic Acids Res. (1997) 25(5)
tRNAscan-SE
tRNAscan algorithm
* screen for putative box A and box b motifs
* then call the computationally more costly structure validation
All we need to do is to take the tRNAscan FALSE POSITVES!
![Page 86: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/86.jpg)
Yes, there is!
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.Nucleic Acids Res. (1997) 25(5)
tRNAscan-SE
tRNAscan algorithm
* screen for putative box A and box b motifs
* then call the computationally more costly structure validation
All we need to do is to take the tRNAscan FALSE POSITVES!
snoRNAs and snoRNA predictions
Screen 200 nt upstream of each known snoRNA to identify those that have tRNA-like promoters
Screen 200 nt upstream of snoReporthits in P. pacificus to lend some hitsadditional reliability
![Page 87: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/87.jpg)
Yes, there is!
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.Nucleic Acids Res. (1997) 25(5)
tRNAscan-SE
tRNAscan algorithm
* screen for putative box A and box b motifs
* then call the computationally more costly structure validation
All we need to do is to take the tRNAscan FALSE POSITVES!
snoRNAs and snoRNA predictions
Screen 200 nt upstream of each known snoRNA to identify those that have tRNA-like promoters
Screen 200 nt upstream of snoReporthits in P. pacificus to lend some hitsadditional reliability
Genome-wide scale
Take tRNAscan FP-hits
Cut out 70 nt down stream or search for poly T stretch
Call blastlcust and look atinter-species clusters
![Page 88: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/88.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 89: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/89.jpg)
Idea
?
!
STARTLeipzig, 1. 6. 2009
FINISHVienna, 1. 10. 2009
RNAz
!
![Page 90: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/90.jpg)
Thanks to the whole Bierinformatik!
![Page 91: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/91.jpg)
Thanks to the whole Bierinformatik!
MOTIVATIONSupport on almost
everything I worked on
![Page 92: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/92.jpg)
Thanks to the whole Bierinformatik!
Talking about RNA, “Gott und
die Welt” ...
MOTIVATIONSupport on almost
everything I worked on
![Page 93: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/93.jpg)
Thanks to the whole Bierinformatik!
MOTIVATIONSupport on almost
everything I worked on
For being the “Mr. Nice Guy “
at my back
Talking about RNA, “Gott und
die Welt” ...
![Page 94: 17 ½ Weeks in Leipzig, Saxonia · Leipzig, 1. 6. 2009 FINISH Vienna, 1. 10. 2009 RNAz! Yes, there is! Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer](https://reader035.fdocuments.net/reader035/viewer/2022081522/5fc38d5de27c6128801893b8/html5/thumbnails/94.jpg)
Thanks to the whole Bierinformatik!
MOTIVATIONSupport on almost
everything I worked on
For being the “Mr. Nice Guy “
at my back
For being PeterF. Stadler
Talking about RNA, “Gott und
die Welt” ...