88 Biosequence PPTs View free & download

Efficient Exact p-Value Computation and Applications to Biosequence Analysis PowerPoint PPT Presentation

Efficient Exact p-Value Computation and Applications to Biosequence Analysis - Milestones due today. Anything to report? http://cs273a.stanford.edu [Bejerano Fall09/10]*

Milestones due today. Anything to report? http://cs273a.stanford.edu [Bejerano Fall09/10]*

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Searching in Applications Containing BioSequences PowerPoint PPT Presentation

Searching in Applications Containing BioSequences - Non-affine: a single gap penalty value is applied to any unmatched residue. Affine: a penalty for a gap is calculated as gapop gapext*l, where gapop is the ...

Non-affine: a single gap penalty value is applied to any unmatched residue. Affine: a penalty for a gap is calculated as gapop gapext*l, where gapop is the ...

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Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases PowerPoint PPT Presentation

Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases - Prune irrelevant data, I/O for non-pruned entries calculate exact values for non ... WD2 has very good performance in k-NN even though not so well pruning ...

Prune irrelevant data, I/O for non-pruned entries calculate exact values for non ... WD2 has very good performance in k-NN even though not so well pruning ...

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Biosequence Similarity Search on the Mercury System PowerPoint PPT Presentation

... Computer Science and Engineering, Washington University in Saint Louis, MO ... Washington University in St. Louis. Slide # 3. Basic Local Alignment Search Tool ...

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Systems Used: PowerPoint PPT Presentation

Systems Used: - Xilinx FPGA on PCI-X bus in Altix Tools Used: Mentor s Modelsim ... Encryption/decryption Structured record search Biosequence search Science data mining

Xilinx FPGA on PCI-X bus in Altix Tools Used: Mentor s Modelsim ... Encryption/decryption Structured record search Biosequence search Science data mining

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Author: Jason Weston et., al PowerPoint PPT Presentation

Author: Jason Weston et., al - Search biosequences from online ... Use protein 3-D structure database SCOP as golden standard. ... 7329 protein domains with known 3D structure on SCOP. ...

Search biosequences from online ... Use protein 3-D structure database SCOP as golden standard. ... 7329 protein domains with known 3D structure on SCOP. ...

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Suffix Trees PowerPoint PPT Presentation

Suffix Trees - Suffix Trees. Lecture 11: October 6, 2005. Algorithms in Biosequence Analysis ... Can amortize cost of text preprocessing over many patterns. 3. O(m) build algorithms ...

Suffix Trees. Lecture 11: October 6, 2005. Algorithms in Biosequence Analysis ... Can amortize cost of text preprocessing over many patterns. 3. O(m) build algorithms ...

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Workshop on Bioinformatics: Tools in Biosequence analysis and biocomputing - Bioinformatics Division Amity Institute of Biotechnology Sector-125, Noida ... medical, behavioral or health data,including those to acquire, store, organize, ...

Bioinformatics Division Amity Institute of Biotechnology Sector-125, Noida ... medical, behavioral or health data,including those to acquire, store, organize, ...

Facilitating%20Standardization%20and%20Exchange%20of%20Array%20Design%20MAGEML2ADF PowerPoint PPT Presentation

Facilitating%20Standardization%20and%20Exchange%20of%20Array%20Design%20MAGEML2ADF - ADF creator module. Common tool module. File reader/writer. Configuration. Update. Logging ... ADF Data - MAGE object (MAGE-stk) MAGE object (MAGE-stk) - ADF Data ...

ADF creator module. Common tool module. File reader/writer. Configuration. Update. Logging ... ADF Data - MAGE object (MAGE-stk) MAGE object (MAGE-stk) - ADF Data ...

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Biomolecular Sequence Analysis RFP Revised Submission Preliminary Presentation PowerPoint PPT Presentation

Biomolecular Sequence Analysis RFP Revised Submission Preliminary Presentation - readonly attribute unsigned long length; readonly attribute Basis basis; ... IN, // Single point in the range [ offset, offset length ] ...

readonly attribute unsigned long length; readonly attribute Basis basis; ... IN, // Single point in the range [ offset, offset length ] ...

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Liquid Architecture PowerPoint PPT Presentation

Liquid Architecture - Configurable architecture that can adapt to needs of particular application ... Reconfigure FPX hardware via Internet and upload system software. ...

Configurable architecture that can adapt to needs of particular application ... Reconfigure FPX hardware via Internet and upload system software. ...

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Patents e-Filing Update PowerPoint PPT Presentation

Patents e-Filing Update - CD-ROM Submissions. Computer Program Listings. CD required for over 300 lines ... Must be CD-ROM or CD-R. See 37 CFR 1.52(e) for details. 34. Future Electronic ...

CD-ROM Submissions. Computer Program Listings. CD required for over 300 lines ... Must be CD-ROM or CD-R. See 37 CFR 1.52(e) for details. 34. Future Electronic ...

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AI and Bioinformatics PowerPoint PPT Presentation

AI and Bioinformatics - In 1973, Herbert Boyer and Stanely Cohen invented DNA cloning. ... In 1981 The Smith-Waterman algorithm for sequence alignment is published ...

In 1973, Herbert Boyer and Stanely Cohen invented DNA cloning. ... In 1981 The Smith-Waterman algorithm for sequence alignment is published ...

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Pairwise alignment PowerPoint PPT Presentation

Pairwise alignment - C G P S A T D E N Q H K R V M I L F Y W. BLOSUM62. G 7. P -2 9. D -1 -1 7. E -2 0 2 6. N 0 -2 2 0 6 ... Q K R S T A M V I L F Y W C. The genetic code ...

C G P S A T D E N Q H K R V M I L F Y W. BLOSUM62. G 7. P -2 9. D -1 -1 7. E -2 0 2 6. N 0 -2 2 0 6 ... Q K R S T A M V I L F Y W C. The genetic code ...

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Artificial Intelligence (AI) PowerPoint PPT Presentation

Artificial Intelligence (AI) - Artificial Intelligence (AI) Addition to the lecture 11

Artificial Intelligence (AI) Addition to the lecture 11

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SMD Data Analysis Tutorial PowerPoint PPT Presentation

SMD Data Analysis Tutorial - Each spot will be individually assessed as specified, prior to any ... to renormalizing each array, using the spots that pass the spot filter criteria. ...

Each spot will be individually assessed as specified, prior to any ... to renormalizing each array, using the spots that pass the spot filter criteria. ...

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Exact String Search PowerPoint PPT Presentation

Exact String Search - For pattern P, position i, let spi(P) be the length of the ... Knuth-Morris-Pratt psuedo-code. Using failure functions. Extentions / strong vs weak shift rule ...

For pattern P, position i, let spi(P) be the length of the ... Knuth-Morris-Pratt psuedo-code. Using failure functions. Extentions / strong vs weak shift rule ...

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OntologyEntry in MAGE PowerPoint PPT Presentation

OntologyEntry in MAGE - Relation of the MGED Ontology to MAGE. Brief review ... Thoracic Oncology. Tumor Bank. Cell Type. Epithelial Cell. Sample ID. AD145. Sex. Male. Organism Status ...

Relation of the MGED Ontology to MAGE. Brief review ... Thoracic Oncology. Tumor Bank. Cell Type. Epithelial Cell. Sample ID. AD145. Sex. Male. Organism Status ...

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MB280 Introduction to Bioinformatics 3 credits Genes, machines and you' Learn the basics of analyzin PowerPoint PPT Presentation

MB280 Introduction to Bioinformatics 3 credits Genes, machines and you' Learn the basics of analyzin - ... of analyzing DNA and protein sequences using state of the art computer software ... 10/11/07 7th Lab Assignment: i. Read the Phylip HTML pages/go to the ...

... of analyzing DNA and protein sequences using state of the art computer software ... 10/11/07 7th Lab Assignment: i. Read the Phylip HTML pages/go to the ...

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BASIC OUTLINE OF CLASS PowerPoint PPT Presentation

BASIC OUTLINE OF CLASS - BASIC OUTLINE OF CLASS. 1) Speculation and research on the origin of life. ... 3) Polyphyletic: does not include the. common ancestor in the group ...

BASIC OUTLINE OF CLASS. 1) Speculation and research on the origin of life. ... 3) Polyphyletic: does not include the. common ancestor in the group ...

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Standards for Proteomics Data PowerPoint PPT Presentation

Standards for Proteomics Data - XML Standards for Proteomics Data. Andrew Jones, Dr Jonathan ... Parasitology research group. Investigating host-parasite response with Toxoplasma gondii ...

XML Standards for Proteomics Data. Andrew Jones, Dr Jonathan ... Parasitology research group. Investigating host-parasite response with Toxoplasma gondii ...

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Exporting MAGEML from the Stanford Microarray Database Using Perl MAGEstk PowerPoint PPT Presentation

Exporting MAGEML from the Stanford Microarray Database Using Perl MAGEstk - Exporting MAGE-ML from the Stanford Microarray Database Using Perl MAGE-stk ... Generated by single method to ensure uniformity ...

Exporting MAGE-ML from the Stanford Microarray Database Using Perl MAGE-stk ... Generated by single method to ensure uniformity ...

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Phylogenetic Shadowing PowerPoint PPT Presentation

Phylogenetic Shadowing - The human genome contains about 3 billion base pairs! Algorithms to analyze these sequences must be ... Internal nodes are the common ancestor (unobserved) ...

The human genome contains about 3 billion base pairs! Algorithms to analyze these sequences must be ... Internal nodes are the common ancestor (unobserved) ...

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Parallel Computation in Biological Sequence Analysis PowerPoint PPT Presentation

Parallel Computation in Biological Sequence Analysis - Each of the N processors performs sequence search in its own bucket ... Three different groups of immunoglobulin sequences from Kabat Database (Beta Release 5.0) ...

Each of the N processors performs sequence search in its own bucket ... Three different groups of immunoglobulin sequences from Kabat Database (Beta Release 5.0) ...

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Factors Influencing Soil Formation PowerPoint PPT Presentation

Factors Influencing Soil Formation - LECTURE 3 Factors Influencing Soil Formation Biota & Time Processes of soil formation Definitions Percolation (J.B. Thompson) Truncated soil (A.I. Bennett) The ...

LECTURE 3 Factors Influencing Soil Formation Biota & Time Processes of soil formation Definitions Percolation (J.B. Thompson) Truncated soil (A.I. Bennett) The ...

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Bioinformatics Research Overview PowerPoint PPT Presentation

Bioinformatics Research Overview - Bioinformatics Research Overview. Li Liao. Develop new algorithms and (statistical) ... Drug discovery. Methods: Put data into a context: knowledge/data ...

Bioinformatics Research Overview. Li Liao. Develop new algorithms and (statistical) ... Drug discovery. Methods: Put data into a context: knowledge/data ...

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Hidden Markov Model: An Introduction PowerPoint PPT Presentation

Hidden Markov Model: An Introduction - (Alignment) Trained model can provide the most likely ... HMMER: calibrate a hidden Markov model. HMM file: lipocalins.hmm. Length ... EG a t P lK Sf ...

(Alignment) Trained model can provide the most likely ... HMMER: calibrate a hidden Markov model. HMM file: lipocalins.hmm. Length ... EG a t P lK Sf ...

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The%20Design%20and%20Application%20of%20Berkeley%20Emulation%20Engines PowerPoint PPT Presentation

The%20Design%20and%20Application%20of%20Berkeley%20Emulation%20Engines - Emulation capacity of 10 Million ASIC gate-equivalents ... 19' Rack Cabin Capacity. 40 compute modules in 5 chassis (8U) per rack ~40TeraOPS, ~1.5TeraFLOPS ...

Emulation capacity of 10 Million ASIC gate-equivalents ... 19' Rack Cabin Capacity. 40 compute modules in 5 chassis (8U) per rack ~40TeraOPS, ~1.5TeraFLOPS ...

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TRACTS Trajectory Classification using Time Series PowerPoint PPT Presentation

TRACTS Trajectory Classification using Time Series - TRACTSTrajectory Classification using Time Series. Aluno: Irineu Junior Pinheiro dos Santos. Orientador:Luis Ot vio de Campos lvares

TRACTSTrajectory Classification using Time Series. Aluno: Irineu Junior Pinheiro dos Santos. Orientador:Luis Ot vio de Campos lvares

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SMD Data Analysis Tutorial - Using a genelist limits the data analyzed to a subset of genes ... Many data are removed, since only those that were very intense in the yellow ...

Using a genelist limits the data analyzed to a subset of genes ... Many data are removed, since only those that were very intense in the yellow ...

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Fast Exact String Matching On the GPU PowerPoint PPT Presentation

Fast Exact String Matching On the GPU - 768 MB total on board RAM. 2D Texture Cache for large readonly data ... Comparing running time of (serial) CPU versus (parallel) GPU programs. CPU: 3.0 GHz Intel Xeon ...

768 MB total on board RAM. 2D Texture Cache for large readonly data ... Comparing running time of (serial) CPU versus (parallel) GPU programs. CPU: 3.0 GHz Intel Xeon ...

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Parallel Computation in Biological Sequence Analysis - Unsorted portion method first load balancing technique ... Apparently, Berger-Munson method provides more accurate alignments with ...

Unsorted portion method first load balancing technique ... Apparently, Berger-Munson method provides more accurate alignments with ...

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MAGE and MAD or MAD about MAGE PowerPoint PPT Presentation

MAGE and MAD or MAD about MAGE - Experiment = 1 Slide 2 Probes. Expression table is huge; must re-index frequently ... Probe Data. Studies, Experiments, and Replicates. Experiment. Study. Hyb ...

Experiment = 1 Slide 2 Probes. Expression table is huge; must re-index frequently ... Probe Data. Studies, Experiments, and Replicates. Experiment. Study. Hyb ...

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Facilitating Standardization and Exchange of Array Design PowerPoint PPT Presentation

Facilitating Standardization and Exchange of Array Design - Checking lists (composite) CompositeSequence. File/Data structure checklist: ... Column order is correct (non mandatory) Data/file content checklist ...

Checking lists (composite) CompositeSequence. File/Data structure checklist: ... Column order is correct (non mandatory) Data/file content checklist ...

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Molecular Biology Primer PowerPoint PPT Presentation

Molecular Biology Primer - DNA encodes the fundamental information required for life ... flourish in immortal youth, unhurt amid the war of elements, the wreck of matter ...

DNA encodes the fundamental information required for life ... flourish in immortal youth, unhurt amid the war of elements, the wreck of matter ...

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Genome database PowerPoint PPT Presentation

Genome database - Talk doc at http://iubio.bio.indiana.edu/daphnia/docs/ genome ... Drosophila: FlyBase, http://flybase.net ... Saccaromyces: SGD, http://genome-www.stanford. ...

Talk doc at http://iubio.bio.indiana.edu/daphnia/docs/ genome ... Drosophila: FlyBase, http://flybase.net ... Saccaromyces: SGD, http://genome-www.stanford. ...

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G2G - Frustrated biologist. DNA seq (Mac), Standen(Unix/Sun), EMBL (VAX/VMS) camel.tar.gz ... most effective? Efforts of both biologists and technoligists. Punchline ...

Frustrated biologist. DNA seq (Mac), Standen(Unix/Sun), EMBL (VAX/VMS) camel.tar.gz ... most effective? Efforts of both biologists and technoligists. Punchline ...

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The ArrayExpress Gene Expression Database: a Software Engineering and Implementation Perspective PowerPoint PPT Presentation

The ArrayExpress Gene Expression Database: a Software Engineering and Implementation Perspective - ... diagram. ArrayExpress ... pressure to bring system online quickly. Use object ... 15 000 000 000 data points. NetCDF. Data warehouse schema. What ...

... diagram. ArrayExpress ... pressure to bring system online quickly. Use object ... 15 000 000 000 data points. NetCDF. Data warehouse schema. What ...

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Gene Prediction PowerPoint PPT Presentation

Gene Prediction - Use 'gene structure' to predict transcripts and polypeptide (protein) sequences ... Dog MHC class II region so far (Doberman) RefSeq at NCBI ...

Use 'gene structure' to predict transcripts and polypeptide (protein) sequences ... Dog MHC class II region so far (Doberman) RefSeq at NCBI ...

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Alignment of Pairs of Sequences 1 PowerPoint PPT Presentation

Alignment of Pairs of Sequences 1 - Ends free-space alignment. Gap penalty. Affine gap penalty. 1) Global alignment ... http://www.paracel.com/products/gm2.html. Group presentation. Wednesday, 12/08/07 ...

Ends free-space alignment. Gap penalty. Affine gap penalty. 1) Global alignment ... http://www.paracel.com/products/gm2.html. Group presentation. Wednesday, 12/08/07 ...

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Pattern Discovery in Bioinformatics Jaak Vilo vilout'ee http:biit'cs'ut'ee - Pattern Discovery in Bioinformatics Jaak Vilo vilout'ee http:biit'cs'ut'ee

Pattern Discovery in Bioinformatics Jaak Vilo vilout'ee http:biit'cs'ut'ee

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Suffix Arrays PowerPoint PPT Presentation

Suffix Arrays - The space requirements of suffix trees can become prohibitive. Kurtz seems to be the king of small suffix trees: 20n n bytes ... Eschew redundant comparisons ...

The space requirements of suffix trees can become prohibitive. Kurtz seems to be the king of small suffix trees: 20n n bytes ... Eschew redundant comparisons ...

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Bioinformatics for Genome data PowerPoint PPT Presentation

Bioinformatics for Genome data - Bioinformatics is the field of science in which biology, computer science, and ... Mouse: MGD, http://www.informatics.jax.org ...

Bioinformatics is the field of science in which biology, computer science, and ... Mouse: MGD, http://www.informatics.jax.org ...

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Digital Libraries INFO 653 Week 6 Xia Lin College of Information Science and Technology Drexel University PowerPoint PPT Presentation

Digital Libraries INFO 653 Week 6 Xia Lin College of Information Science and Technology Drexel University - Creating a Framework of Guidance for Building Good Digital Collections (2002) ... cosmonaut. spationaut. taikonaut. Synonym Rings ...

Creating a Framework of Guidance for Building Good Digital Collections (2002) ... cosmonaut. spationaut. taikonaut. Synonym Rings ...

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MGED Ontology PowerPoint PPT Presentation

MGED Ontology - Core ontology does not cover all of MAGE or contain all MAGE associations. ... When Ontology needed but no direct association, used describable (if describable) ...

Core ontology does not cover all of MAGE or contain all MAGE associations. ... When Ontology needed but no direct association, used describable (if describable) ...

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Argos - Argos is a framework for distributing common components with implemented genome data systems ... docs/ & install/ -- Argos instructions and usage ...

Argos is a framework for distributing common components with implemented genome data systems ... docs/ & install/ -- Argos instructions and usage ...

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The FDK Unit Scientific Advisory Board Meeting PowerPoint PPT Presentation

The FDK Unit Scientific Advisory Board Meeting - Other postgrad students 1 3 4 2 2 4. Other academic 10 - 10 10 1 11. Auxiliary personnel ... Other postgrad students 2 1 3 2 1 3. Other academic 3 - 3 1 - 1 ...

Other postgrad students 1 3 4 2 2 4. Other academic 10 - 10 10 1 11. Auxiliary personnel ... Other postgrad students 2 1 3 2 1 3. Other academic 3 - 3 1 - 1 ...

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Population Genetics Introduction PowerPoint PPT Presentation

Population Genetics Introduction - Population genetics uses statistics to understand how genetics affects large ... A and a, B and b. Paternal haplotype has A and B, Maternal haplotype has a and b ...

Population genetics uses statistics to understand how genetics affects large ... A and a, B and b. Paternal haplotype has A and B, Maternal haplotype has a and b ...

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Aplica - Aplica o de Arquiteturas Reconfigur veis para Algoritmos de Bioinform tica Jan M. Corr a (doutorando no ENE) Alba C. M. A. Melo Terceiro Semin rio Informal ...

Aplica o de Arquiteturas Reconfigur veis para Algoritmos de Bioinform tica Jan M. Corr a (doutorando no ENE) Alba C. M. A. Melo Terceiro Semin rio Informal ...

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The From Data to Knowledge FDK Research Unit a National Center of Excellence PowerPoint PPT Presentation

The From Data to Knowledge FDK Research Unit a National Center of Excellence - The From Data to Knowledge (FDK) Research Unit a National ... Antonin Doucet: Advanced document description, a sequential approach. postdoc at INRIA, France ...

The From Data to Knowledge (FDK) Research Unit a National ... Antonin Doucet: Advanced document description, a sequential approach. postdoc at INRIA, France ...

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Bioinformatics Course Outline PowerPoint PPT Presentation

Bioinformatics Course Outline - Homologue finding, sequence alignment, multiple alignment, phylogeny trees. 2 ... Homologues: Orthology vs Paralogy. Reproduced from NCBI education website. Intro. ...

Homologue finding, sequence alignment, multiple alignment, phylogeny trees. 2 ... Homologues: Orthology vs Paralogy. Reproduced from NCBI education website. Intro. ...

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An evaluation of representing proteomics experiments within FuGE-OM PowerPoint PPT Presentation

An evaluation of representing proteomics experiments within FuGE-OM - Demonstrate correspondence with PSI-OM (and PEDRo) for experiment, lab procedures etc. Does FuGE-OM give additional features to the models? ...

Demonstrate correspondence with PSI-OM (and PEDRo) for experiment, lab procedures etc. Does FuGE-OM give additional features to the models? ...

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Similarity Score Significance PowerPoint PPT Presentation

We saw last time how the alignment score is a log likelihood of H vs R ... However, we are rarely considering just one alignment. ...

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Exporting MAGEML from the Stanford Microarray Database Using Perl MAGEstk - Close correspondences were easy (Person) Bad matches were problematic (FactorValues) ... Create a blank Experiment object, and add the ExperimentDesign, and pass the ...

Close correspondences were easy (Person) Bad matches were problematic (FactorValues) ... Create a blank Experiment object, and add the ExperimentDesign, and pass the ...

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Biology Image Libraries PowerPoint PPT Presentation

Biology Image Libraries - The ultimate goal is to enable discovery of new biological insights... Slides at http://chipmunk.bio.indiana.edu/~gilbertd/about/talks ...

The ultimate goal is to enable discovery of new biological insights... Slides at http://chipmunk.bio.indiana.edu/~gilbertd/about/talks ...

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Hidden Markov Models PowerPoint PPT Presentation

Hidden Markov Models - pLoaded(Fair) = 0.10, pLoaded(Loaded) = 0.90, eFair(1) = 1/6, ..., eFair(6) = 1/6 ... Loaded. 0.05. 0.10. 0.90. 0.95. 17. HMM structure. min length = 7, ...

pLoaded(Fair) = 0.10, pLoaded(Loaded) = 0.90, eFair(1) = 1/6, ..., eFair(6) = 1/6 ... Loaded. 0.05. 0.10. 0.90. 0.95. 17. HMM structure. min length = 7, ...

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Biosequence PowerPoint PPT Presentations