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

Jan 16, 2024 •450 likes •613 views

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

V3 Loop Sequence Space Analysis Kasia Bo ż ek bozek@mpi-inf.mpg.de Max-Planck Institute für Informatik, Saarbrücken AREVIR Bonn 24.04.2009
V3 loop sequence space analysis selection of V3 loop sequence variants 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 Bonn 24.04.2008
Data analysis Approach 2 sets of sequences from Los Alamos NSI/ SI CCR5/ CXCR4/ R5X4 distance distribution phylogenetical analysis using Splitstree hierarchical clustering Kasia Bo ż ek AREVIR Bonn 24.04.2008
Distance distribution – NSI/ SI NSI-NSI NSI-SI SI-SI Kasia Bo ż ek AREVIR Bonn 24.04.2008
Distance distribution – R5/ X4 R5-R5 R5X4-R5X4 X4-X4 Kasia Bo ż ek AREVIR Bonn 24.04.2008
Phylogenetical analysis - Splitstree 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 Splitstree – a tree-like network visualizing conflicting phylogenies Kasia Bo ż ek AREVIR Bonn 24.04.2008
Phylogenetical analysis - Splitstree Phylogenetical analysis Kasia Bo ż ek AREVIR meeting Bonn 24.04.2008
Hierarchical clustering Kasia Bo ż ek AREVIR Bonn 24.04.2008
Hierarchical clustering NSI R5 R5X4 SI X4 Kasia Bo ż ek AREVIR Bonn 24.04.2008
V3 loop sequence space analysis R5/ NSI: X4/ SI: conserved diverse forming clusters placed in distant parts of sequence space slow disease progression disease immune component of the V3 loop evolutionary pattern? R5/ NSI sequences under purifying selection of the immune system? Kasia Bo ż ek AREVIR Bonn 24.04.2008
Sequence space location vs. CD4 + T-cells Kasia Bo ż ek AREVIR Bonn 24.04.2008
Sequence space location vs. CD4 + T-cells 4 3 1 2 Kasia Bo ż ek AREVIR Bonn 24.04.2008
Conclusions conservation of CCR5/ NSI V3 loop sequences high variability of CXCR4/ SI viruses possible immune system selection pressure Kasia Bo ż ek AREVIR Bonn 24.04.2008
Conclusion Acknowledgements Alexander Thielen Rolf Kaiser Oliver Sander Saleta Sierra Aragon André Altmann Thomas Lengauer
Conclusion

Download Presentation

Download Policy: The content available on the website is offered to you 'AS IS' for your personal information and use only. It cannot be commercialized, licensed, or distributed on other websites without prior consent from the author. To download a presentation, simply click this link. If you encounter any difficulties during the download process, it's possible that the publisher has removed the file from their server.

Recommend

V3 Loop Sequence Space Analysis Kasia Bo ek bozek@mpi-inf.mpg.de MPI Saarbrcken AREVIR

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

812 views • 34 slides

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 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 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

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 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 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.

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

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:

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

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

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 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 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 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

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

School to Heart to Home Conscious Discipline Parent Workshop Series 1. Composure The 7 2.

School to Heart to Home Conscious Discipline Parent Workshop Series 1. Composure The 7 2. Assertiveness 3. Encouragement Powers of 4. Choices Conscious 5. Empathy Adults 6. Positive Intent 7. Consequences Quick Review... Survival

594 views • 25 slides

Literacy Information session for parents Holmesdale Infant School March 2017 Literacy in the

Literacy Information session for parents Holmesdale Infant School March 2017 Literacy in the Early Years Children learn through lots of different ways, playing, listening, watching, recording, working in groups and most importantly

325 views • 28 slides

Tips for Successful Field Experiences Send a letter home explaining your study and include

Tips for Successful Field Experiences Send a letter home explaining your study and include tentative dates for field work Prepare your field site- check for any hazards. Make sure all students visit the restroom before leaving Practice data

538 views • 22 slides

ADVANCED ACADEMIC PROGRAMS POPLAR TREE ELEMENTARY SCHOOL SPRING 2018 Philosophy What educators

ADVANCED ACADEMIC PROGRAMS POPLAR TREE ELEMENTARY SCHOOL SPRING 2018 Philosophy What educators and psychologists recognize as giftedness in children is really potential giftedness, which denotes promise rather than fulfillment and probabilities

495 views • 22 slides

The Google File System Joanna Swietlicka October 13, 2010 Joanna Swietlicka The Google

Design overview Interactions Master operation Fault tolerance and diagnosis Measurements The Google File System Joanna Swietlicka October 13, 2010 Joanna Swietlicka The Google File System Design overview Interactions Master

622 views • 45 slides

National collaboration on new materials from the forest och std fr Treesearch is a

National collaboration on new materials from the forest och std fr Treesearch is a collaboration platform forskningen that gathers and supports research A platform where academy, industry, private foundations and the government creates an

422 views • 14 slides

SEAWALL UPGRADES FINAL DESIGN UPDATE Park Board Committee Meeting November 14, 2016 Purpose of

SOUTH FALSE CREEK SEAWALL UPGRADES FINAL DESIGN UPDATE Park Board Committee Meeting November 14, 2016 Purpose of Presentation To report back to the Board regarding details of the final designs for improvements to the South False Creek

506 views • 22 slides

Roslindale Village Walk Assessment Walk Assessment Introduce all participants Discuss basics of

Roslindale Village Walk Assessment Walk Assessment Introduce all participants Discuss basics of walking infrastructure Walk through Roslindale Village Discuss observations and recommend improvements Next Steps: Review report/submit comments

375 views • 19 slides