v3 loop sequence space analysis
play

V3 Loop Sequence Space Analysis Kasia Bo ek bozek@mpi-inf.mpg.de - PowerPoint PPT Presentation

Sep 24, 2022 •463 likes •812 views

V3 Loop Sequence Space Analysis Kasia Bo ek bozek@mpi-inf.mpg.de MPI Saarbrcken AREVIR meeting, Bonn 11.04.2008 V3 loop highly variable genome sequence related to coreceptor usage CCR5-CXCR4 coreceptor switch related to rapid disease

  1. V3 Loop Sequence Space Analysis Kasia Bo ż ek bozek@mpi-inf.mpg.de MPI Saarbrücken AREVIR meeting, Bonn 11.04.2008

  2. V3 loop highly variable genome sequence related to coreceptor usage CCR5-CXCR4 coreceptor switch related to rapid disease progression importance of coreceptor prediction Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  3. Coreceptor prediction in-silico phenotypic assays Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  4. V3 loop sequence space analysis selection of sequences for experimental imaging of the HIV cell entry understanding of the distribution of V3 loop sequences in their sequence space Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  5. Approach 2 datasets of sequences from Los Alamos NSI/ SI CCR5/ CXCR4/ R5X4 different distance measures Hamming distance BLOSUM matrix amino acid size and charge mutations on significant positions hierarchical clustering phylogenetical analysis using Splitstree Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  6. NSI vs. NSI Distance distribution SI vs. SI NSI vs. SI Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  7. R5 vs. R5 Distance distribution X4 vs. X4 R5X4 vs. R5X4 Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  8. Sequence clustering Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  9. Sequence clustering Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  10. Sequence clustering Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  11. Sequence clustering Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  12. Sequence clustering NSI R5 R5X4 SI X4 Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  13. Phylogenetical analysis evolution - not always is a branching tree-like process different phylogenetical signals in real data not always fitting into a unique tree Splitstree – a tree-like network visualizing conflicting phylogenies Splitstree Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  14. Phylogenetical analysis Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  15. Phylogenetical analysis split Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  16. Phylogenetical analysis SI NSI Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  17. Phylogenetical analysis Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  18. Phylogenetical analysis Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  19. Difficult sequences unexpected placement of some sequences on the tree bad annotation? difficult cases? Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  20. Difficult sequences unexpected placement of some sequences on the tree bad annotation? difficult cases? Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  21. Difficult sequences unexpected placement of some sequences on the tree bad annotation? difficult cases? Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  22. Difficult sequences unexpected placement of some sequences on the tree bad annotation? difficult cases? Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  23. Difficult sequences unexpected placement of some sequences on the tree bad annotation? difficult cases? Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  24. Difficult sequences Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  25. Disease and space position selection pressures on the R5 viruses high variability of X4 emergence of X4 and CD4+ T-cell count depletion cause or result of the disease progression? Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  26. Disease and space position 2 possible scenarios: immune system fail precedes the coreceptor switch coreceptor switch anticipates the disease Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  27. Disease and space position 2 possible scenarios: immune system fail precedes the coreceptor switch coreceptor switch anticipates the disease Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  28. Disease and space position 2 possible scenarios: immune system fail precedes highly mutated viruses only in the coreceptor switch cases of low CD4+ cell count coreceptor switch anticipates the disease Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  29. Disease and space position 2 possible scenarios: immune system fail precedes highly mutated viruses only in the coreceptor switch cases of low CD4+ cell count coreceptor switch anticipates the disease Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  30. Disease and space position 2 possible scenarios: immune system fail precedes highly mutated viruses only in the coreceptor switch cases of low CD4+ cell count coreceptor switch anticipates the disease mutated viruses within all levels of CD4+ cell count Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  31. Disease and space position Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  32. Disease and space position Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  33. Conclusions conservation of CCR5 V3 loop sequences highly variable CXCR4 viruses association to the immune escape scenario Kasia Bo ż ek AREVIR meeting Bonn 11.04.2008

  34. Conclusion Acknowledgements Alexander Thielen Rolf Kaiser Oliver Sander Saleta Sierra Aragon André Altmann Thomas Lengauer

Recommend

V3 Loop Sequence Space Analysis Kasia Bo ek bozek@mpi-inf.mpg.de Max-Planck Institute fr

V3 Loop Sequence Space Analysis Kasia Bo ek bozek@mpi-inf.mpg.de Max-Planck Institute fr

V3 Loop Sequence Space Analysis Kasia Bo ek bozek@mpi-inf.mpg.de Max-Planck Institute fr Informatik, Saarbrcken AREVIR Bonn 24.04.2009 V3 loop sequence space analysis selection of V3 loop sequence variants for experimental imaging of

613 views • 15 slides
SEQUENCE ANALYSIS The term " sequence analysis " in biology implies subjecting a DNA or

SEQUENCE ANALYSIS The term " sequence analysis " in biology implies subjecting a DNA or

Sequence Analysis SEQUENCE ANALYSIS The term " sequence analysis " in biology implies subjecting a DNA or peptide sequence to sequence alignment, sequence databases, repeated sequence searches, or other bioinformatics methods on a

818 views • 20 slides
CSE182-L16 Non-coding RNA Biol. Data analysis: Review Assembly Protein Sequence Sequence

CSE182-L16 Non-coding RNA Biol. Data analysis: Review Assembly Protein Sequence Sequence

CSE182-L16 Non-coding RNA Biol. Data analysis: Review Assembly Protein Sequence Sequence Analysis Analysis Gene Finding Much other analysis is possible Assembly Genomic Analysis/ Pop. Genetics Protein Sequence Sequence Analysis

814 views • 35 slides
Asynchronous sequence circuits An asynchronous sequence machine is a sequence circuit without

Asynchronous sequence circuits An asynchronous sequence machine is a sequence circuit without

Asynchronous sequence circuits An asynchronous sequence machine is a sequence circuit without flip-flops Asynchronous sequence machines are based on combinational gates with feedback Upon analysis it is assumed : Only one signal at a

1.34k views • 66 slides
1 Unroll and Jam Unroll and Jam Example (cont) Unroll the Outer Loop Idea do j = 1,2*n by 2

1 Unroll and Jam Unroll and Jam Example (cont) Unroll the Outer Loop Idea do j = 1,2*n by 2

Tiling: A Data Locality Optimizing Algorithm Loop Unrolling Motivation Previously Reduces loop overhead Kelly & Pugh transformation framework Improves effectiveness of other transformations Affine space partitions for

45 views • 4 slides
Analysis of DNA Sequence Data Using Freeware Programs: Sequencher 4.9 Sequence Scanner 1.0

Analysis of DNA Sequence Data Using Freeware Programs: Sequencher 4.9 Sequence Scanner 1.0

Analysis of DNA Sequence Data Using Freeware Programs: Sequencher 4.9 Sequence Scanner 1.0 Daniel Williams willida@shelterisland.k12.ny.us Its possible that you have received your sequence data directly from the Sequencing Lab in Word Pad

589 views • 30 slides
Sequence Alignment: Linear Space Q. Can we avoid using quadratic space? Easy. Optimal value in

Sequence Alignment: Linear Space Q. Can we avoid using quadratic space? Easy. Optimal value in

Sequence Alignment: Linear Space Q. Can we avoid using quadratic space? Easy. Optimal value in O(m + n) space and O(mn) time. Compute OPT(i, ) from OPT(i-1, ). No longer a simple way to recover alignment itself. Theorem.

520 views • 10 slides
HMMs for Pairwise Sequence Alignment based on Ch. 4 from Biological Sequence Analysis by R.

HMMs for Pairwise Sequence Alignment based on Ch. 4 from Biological Sequence Analysis by R.

0. HMMs for Pairwise Sequence Alignment based on Ch. 4 from Biological Sequence Analysis by R. Durbin et al., 1998 Acknowledgement: M.Sc. student Oana R at oi [ B. subtilis PRPP synthase ] 1. PLAN 1 How to build a pair HMM for

590 views • 36 slides
MHV amplitudes in N=4 SUSY Yang-Mills theory and quantum geometry of the momentum space Alexander

MHV amplitudes in N=4 SUSY Yang-Mills theory and quantum geometry of the momentum space Alexander

Outline Introduction and tree MHV amplitudes BDS conjecture and amplitude - Wilson loop correspondence c=1 string example and fermionic representation of amplitudes Quantization of the moduli space On the fermionic representation of the loop

422 views • 28 slides
Constant mean curvature surfaces in Minkowski 3-space via loop groups David Brander Now:

Constant mean curvature surfaces in Minkowski 3-space via loop groups David Brander Now:

CMC Surfaces in Euclidean Space CMC surfaces in Minkowski 3-Space Constant mean curvature surfaces in Minkowski 3-space via loop groups David Brander Now: Department of Mathematics Kobe University (From August 2008: Danish Technical

856 views • 63 slides
Pairwise Sequence Alignment based on Ch. 2 from Biological Sequence Analysis by R. Durbin et

Pairwise Sequence Alignment based on Ch. 2 from Biological Sequence Analysis by R. Durbin et

0. Pairwise Sequence Alignment based on Ch. 2 from Biological Sequence Analysis by R. Durbin et al., 1998 Acknowledgements: M.Sc. student Oana R at oi M.Sc. student Diana Popovici [ Sperm whale myoglobin (2lh7) and Lupin leghaemoglobin

1.29k views • 66 slides
1 Legality of Loop Interchange (cont) Loop Interchange Example Case analysis of the direction

1 Legality of Loop Interchange (cont) Loop Interchange Example Case analysis of the direction

Loop Transformations for Parallelism & Locality Loop Permutation Idea Previously Swap the order of two loops to increase parallelism, to improve spatial Data dependences and loops locality, or to enable other transformations

604 views • 5 slides
Analysis and classification of the DNA Analysis and classification of the DNA sequence of TARA

Analysis and classification of the DNA Analysis and classification of the DNA sequence of TARA

Analysis and classification of the DNA Analysis and classification of the DNA sequence of TARA 7S_3634040 sequence of TARA 7S_3634040 Presentation of the DNA sequence Presentation of the DNA sequence Tanger TARA7S_3634040 genomic DNA

312 views • 8 slides
Upper and Lower Loop Bound Estimation by Symbolic Execution and Loop Acceleration Pavel Cadek

Upper and Lower Loop Bound Estimation by Symbolic Execution and Loop Acceleration Pavel Cadek

Upper and Lower Loop Bound Estimation by Symbolic Execution and Loop Acceleration Pavel Cadek 1 1 TU Wien, Austria Formal Methods in Computer-Aided Design 30 Oct - 2 Nov, 2018 Loop Bound Analysis Upper loop bound: max { n , 0 } Lower loop

248 views • 5 slides
Principles of Program Analysis An overview of approaches beyond loop analysis and optimizations

Principles of Program Analysis An overview of approaches beyond loop analysis and optimizations

Principles of Program Analysis An overview of approaches beyond loop analysis and optimizations cs6363 1 The Nature of static analysis --- approximation Static program analysis --- predict the dynamic behavior of programs without running

368 views • 19 slides
Multiple Sequence Alignment based on Ch. 6 from Biological Sequence Analysis by R. Durbin et

Multiple Sequence Alignment based on Ch. 6 from Biological Sequence Analysis by R. Durbin et

0. Multiple Sequence Alignment based on Ch. 6 from Biological Sequence Analysis by R. Durbin et al., 1998 Acknowledgements: M.Sc. student Diana Popovici M.Sc. student Oana R at oi [ MHC class I with peptide ] MHC = Major

726 views • 51 slides
Protein Sequence Analysis Protein Sequence Analysis Protein sequence motifs Protein sequence

Protein Sequence Analysis Protein Sequence Analysis Protein sequence motifs Protein sequence

Protein Sequence Analysis Protein Sequence Analysis Protein sequence motifs Protein sequence motifs Premise: the sequence of a protein Premise: the sequence of a protein sequence gives clues about its structure sequence gives clues

359 views • 11 slides
Coarse-Grained Parallelism Variable Privatization, Loop Alignment, Loop Fusion, Loop

Coarse-Grained Parallelism Variable Privatization, Loop Alignment, Loop Fusion, Loop

Coarse-Grained Parallelism Variable Privatization, Loop Alignment, Loop Fusion, Loop interchange and skewing, Loop Strip-mining cs6363 1 Introduction Our previous loop transformations target vector and superscalar architectures Now

538 views • 32 slides
Repetition Types of Loops Counting loop Know how many times to loop

Repetition Types of Loops Counting loop Know how many times to loop

Repetition Types of Loops Counting loop Know how many times to loop Sentinel-controlled loop Expect specific input value to end loop Endfile-controlled loop End of data file is end of loop Input validation loop

257 views • 8 slides
Trading Strategies Introduction Trading Loop Trading Loop Trading Loop Trading Loop Three

Trading Strategies Introduction Trading Loop Trading Loop Trading Loop Trading Loop Three

Trading Strategies Introduction Trading Loop Trading Loop Trading Loop Trading Loop Three Strategies 1. Mean Reversion 2. Momentum 3. Pairs Trading Budish, E., Cramton, P ., & Shim, J. (2015). The high-frequency trading arms race:

803 views • 22 slides
Loop-invariant code motion Example Two steps: analysis & transformation x := 3 Step 1: find

Loop-invariant code motion Example Two steps: analysis & transformation x := 3 Step 1: find

Loop-invariant code motion Example Two steps: analysis & transformation x := 3 Step 1: find invariant computations in loop y := 4 y := 5 invariant: computes same result each time evaluated z := x * y Step 2: move them outside loop

355 views • 4 slides
1 What Is Control-Flow Analysis? Loop Concepts Control-flow analysis discovers the flow of

1 What Is Control-Flow Analysis? Loop Concepts Control-flow analysis discovers the flow of

Control-Flow Analysis and Loop Detection Context Last time Data-flow Speeding up data-flow analysis Flow of data values from defs to uses Could alternatively be represented as a data dependence Today Control-flow analysis

516 views • 5 slides
A Simple Representation of the Impact of a Loop Heat Pipe on a Space System Perry Ramsey Andrew

A Simple Representation of the Impact of a Loop Heat Pipe on a Space System Perry Ramsey Andrew

A Simple Representation of the Impact of a Loop Heat Pipe on a Space System Perry Ramsey Andrew Hensley ITT Industries Space Systems Division Fort Wayne, IN TFAWS '04 31 August 2004 Abstract Abstract As two phase thermal control

958 views • 21 slides
Sequence to Sequence models: Connectionist Temporal Classification 1 Sequence-to-sequence

Sequence to Sequence models: Connectionist Temporal Classification 1 Sequence-to-sequence

Deep Learning Sequence to Sequence models: Connectionist Temporal Classification 1 Sequence-to-sequence modelling Problem: A sequence goes in A different sequence comes out E.g. Speech recognition:

1.86k views • 172 slides

More recommend