Introduction to Pattern Recognition. Sequence structure function
|
|
- Jade Wright
- 5 years ago
- Views:
Transcription
1 Introduction to Pattern Recognition Sequence structure function Prediction in Bioinformatics What do we want to predict? Features from sequence Data mining How can we predict? Homology / Alignment Pattern Recognition / Statistical Methods / Machine Learning What is prediction? Generalization / Overfitting Preventing overfitting: Homology reduction How do we measure prediction? Performance measures Threshold selection Henrik Nielsen Center for Biological Sequence Analysis Technical University of Denmark Protein-coding genes transcription factor binding sites transcription start/stop translation start/stop splicing: donor/acceptor sites Non-coding RNA trnas rrnas mirnas General features Structure (curvature/bending) Binding (histones etc.) Prediction from DNA sequence Folding / structure Post-Translational Modifications Attachment: phosphorylation glycosylation lipid attachment Cleavage: signal peptides, propeptides, transit peptides Sorting: secretion, import into various organelles, insertion into membranes Interactions Function Enzyme activity Transport Receptors Structural components etc Prediction from amino acid sequence 1
2 Protein sorting in eukaryotes Data: UniProt annotation of protein sorting Annotations relevant for protein sorting are found in: the CC (comments) lines ( Ontology cross-references (DR lines) to GO (Gene the FT (feature table) lines ID INS_HUMAN Reviewed; 110 AA. AC P01308; DE Insulin precursor [Contains: Insulin B chain; Insulin A chain]. GN Name=INS; CC -!- SUBCELLULAR LOCATION: Secreted. DR GO; GO: ; C:extracellular region; IC:UniProtKB. FT SIGNAL 1 24 Proteins belong in different organelles of the cell and some even have their function outside the cell Günter Blobel was in 1999 awarded The Nobel Prize in Physiology or Medicine for the discovery that "proteins have intrinsic signals that govern their transport and localization in the cell" 3 types of non-experimental qualifiers in the CC and FT lines: Potential: Predicted by sequence analysis methods Probable: Inconclusive experimental evidence By similarity: Predicted by alignment to proteins with known location Extreme example: A4_HUMAN, Alzheimer disease amyloid protein Problems in database parsing CC -!- SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane CC protein. Note=Cell surface protein that rapidly becomes CC internalized via clathrin-coated pits. During maturation, the CC immature APP (N-glycosylated in the endoplasmic reticulum) moves CC to the Golgi complex where complete maturation occurs (O- CC glycosylated and sulfated). After alpha-secretase cleavage, CC soluble APP is released into the extracellular space and the C- CC terminal is internalized to endosomes and lysosomes. Some APP CC accumulates in secretory transport vesicles leaving the late Golgi CC compartment and returns to the cell surface. Gamma-CTF(59) peptide CC is located to both the cytoplasm and nuclei of neurons. It can be CC translocated to the nucleus through association with Fe65. Beta- CC APP42 associates with FRPL1 at the cell surface and the complex is CC then rapidly internalized. APP sorts to the basolateral surface in CC epithelial cells. During neuronal differentiation, the Thr-743 CC phosphorylated form is located mainly in growth cones, moderately CC in neurites and sparingly in the cell body. Casein kinase CC phosphorylation can occur either at the cell surface or within a CC post-golgi compartment. DR GO; GO: ; C:cell surface; IDA:UniProtKB. DR GO; GO: ; C:extracellular region; TAS:ProtInc. DR GO; GO: ; C:integral to plasma membrane; TAS:ProtInc. Prediction methods Homology / Alignment Simple pattern recognition Example: PROSITE entry PS00014, ER_TARGET: Endoplasmic reticulum targeting sequence. Pattern: [KRHQSA]-[DENQ]-E-L> Statistical methods Weight matrices: calculate amino acid probabilities Other examples: Regression, variance analysis, clustering Machine learning Like statistical methods, but parameters are estimated by iterative training rather than direct calculation Examples: Neural Networks (NN), Hidden Markov Models (HMM), Support Vector Machines (SVM) 2
3 Prediction of subcellular localisation from sequence Homology: threshold 30%-70% identity Sorting signals ( zip codes ) N-terminal: secretory (ER) signal peptides, mitochondrial & chloroplast transit peptides. C-terminal: peroxisomal targeting signal 1, ER-retention signal. internal: Nuclear localisation signals, nuclear export signals. Global properties amino acid composition, aa pair composition composition in limited regions predicted structure physico-chemical parameters Combined approaches Signal-based prediction Signal peptides von Heijne 1983, 1986 [WM] SignalP (Nielsen et al. 1997, 1998; Bendtsen et al. 2004) [NN, HMM] Mitochondrial & chloroplast transit peptides Mitoprot (Claros & Vincens 1996) [linear discriminant using physico-chemical parameters] ChloroP, TargetP* (Emanuelsson et al. 1999, 2000) [NN] ipsort* (Bannai et al. 2002) [decision tree using physicochemical parameters] Protein Prowler* (Hawkins & Bodén 2006) [NN] *= includes also signal peptides Nuclear localisation signals PredictNLS (Cokol et al. 2000) [regex] NucPred (Heddad et al. 2004) [regex, GA] Composition-based prediction A simple statistical method: Linear regression Nakashima and Nishikawa 1994 [2 categories; odds-ratio statistics] ProtLock (Cedano et al. 1997) [5 categories; Mahalanobis distance] Chou and Elrod 1998 [12 categories; covariant discriminant] NNPSL (Reinhardt and Hubbard 1998) [4 categories; NN] SubLoc (Hua and Sun 2001) [4 categories; SVM] PLOC (Park and Kanehisa 2003) [12 categories; SVM] LOCtree (Nair & Rost 2005) [6 categories; SVM incl. regions, structure and profiles] BaCelLo (Pierleoni et al. 2006) [5 categories; SVM incl. regions and profiles] Pro: does not require knowledge of signals works even if N-terminus is wrong Con: cannot identify isoform differences Observations (training data): a set of x values (input) and y values (output). Model: y = ax + b (2 parameters, which are estimated from the training data) Prediction: Use the model to calculate a y value for a new x value Note: the model does not fit the observations exactly. Can we do better than this? 3
4 Overfitting A classification problem y = ax + b 2 parameter model Good description, poor fit y = ax 6 +bx 5 +cx 4 +dx 3 +ex 2 +fx+g 7 parameter model Poor description, good fit Note: It is not interesting that a model can fit its observations (training data) exactly. To function as a prediction method, a model must be able to generalize, i.e. produce sensible output on new data. How complex a model should we choose? This depends on: The real complexity of the problem The size of the training data set The amount of noise in the data set How to estimate parameters for prediction? Model selection Linear Regression Quadratic Regression Join-the-dots 4
5 The test set method The test set method The test set method The test set method 5
6 The test set method 6
7 7
8 Which kind of? Problem: sequences are related Note: Leave-one-out is also known as jack-knife ALAKAAAAM ALAKAAAAN ALAKAAAAR ALAKAAAAT ALAKAAAAV GMNERPILT GILGFVFTM TLNAWVKVV KLNEPVLLL AVVPFIVSV If the sequences in the test set are closely related to those in the training set, we can not measure true generalization performance Calculate all pairwise similarities in the data set Define a threshold for being neighbours (too closely related) Calculate numbers of neighbours for each example, and remove the example with most neighbours Repeat until there are no examples with neighbours left Solution: Homology reduction Alternative: Homology partitioning keep all examples, but cluster them so that no neighbours end up in the same fold Should be combined with weighting The Hobohm algorithm First approach: two sequences are too closely related, if the prediction problem can be solved by alignment Defining a threshold for homology reduction The Sander/Schneider curve: For protein structure prediction, 70% identical classification of secondary structure means prediction by alignment is possible This corresponds to 25% identical amino acids in a local alignment > 80 positions 8
9 Defining a threshold for homology reduction Second approach: two sequences are too closely related, if their homology is statistically significant The Pedersen / Nielsen / Wernersson curve: Use the extreme value distribution to define the BLAST score at which the similarity is stronger than random 9
Signal peptides and protein localization prediction
Downloaded from orbit.dtu.dk on: Jun 30, 2018 Signal peptides and protein localization prediction Nielsen, Henrik Published in: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics Publication
More informationSupervised Ensembles of Prediction Methods for Subcellular Localization
In Proc. of the 6th Asia-Pacific Bioinformatics Conference (APBC 2008), Kyoto, Japan, pp. 29-38 1 Supervised Ensembles of Prediction Methods for Subcellular Localization Johannes Aßfalg, Jing Gong, Hans-Peter
More informationYeast ORFan Gene Project: Module 5 Guide
Cellular Localization Data (Part 1) The tools described below will help you predict where your gene s product is most likely to be found in the cell, based on its sequence patterns. Each tool adds an additional
More informationProtein Bioinformatics. Rickard Sandberg Dept. of Cell and Molecular Biology Karolinska Institutet sandberg.cmb.ki.
Protein Bioinformatics Rickard Sandberg Dept. of Cell and Molecular Biology Karolinska Institutet rickard.sandberg@ki.se sandberg.cmb.ki.se Outline Protein features motifs patterns profiles signals 2 Protein
More informationCHAPTER 3. Cell Structure and Genetic Control. Chapter 3 Outline
CHAPTER 3 Cell Structure and Genetic Control Chapter 3 Outline Plasma Membrane Cytoplasm and Its Organelles Cell Nucleus and Gene Expression Protein Synthesis and Secretion DNA Synthesis and Cell Division
More informationDivision Ave. High School AP Biology
Tour of the Cell 1 Types of cells Prokaryote bacteria cells - no organelles - organelles Eukaryote animal cells Eukaryote plant cells Why organelles? Specialized structures u specialized functions cilia
More informationWhat is the central dogma of biology?
Bellringer What is the central dogma of biology? A. RNA DNA Protein B. DNA Protein Gene C. DNA Gene RNA D. DNA RNA Protein Review of DNA processes Replication (7.1) Transcription(7.2) Translation(7.3)
More informationChapter 12: Intracellular sorting
Chapter 12: Intracellular sorting Principles of intracellular sorting Principles of intracellular sorting Cells have many distinct compartments (What are they? What do they do?) Specific mechanisms are
More information9/11/18. Molecular and Cellular Biology. 3. The Cell From Genes to Proteins. key processes
Molecular and Cellular Biology Animal Cell ((eukaryotic cell) -----> compare with prokaryotic cell) ENDOPLASMIC RETICULUM (ER) Rough ER Smooth ER Flagellum Nuclear envelope Nucleolus NUCLEUS Chromatin
More information!"#$%&'%()*%+*,,%-&,./*%01%02%/*/3452*%3&.26%&4752*,,*1%%
!"#$%&'%()*%+*,,%-&,./*%01%02%/*/3452*%3&.26%&4752*,,*1%% !"#$%&'(")*++*%,*'-&'./%/,*#01#%-2)#3&)/% 4'(")*++*% % %5"0)%-2)#3&) %%% %67'2#72'*%%%%%%%%%%%%%%%%%%%%%%%4'(")0/./% % 8$+&'&,+"/7 % %,$&7&/9)7$*/0/%%%%%%%%%%
More informationEXAMPLE-BASED CLASSIFICATION OF PROTEIN SUBCELLULAR LOCATIONS USING PENTA-GRAM FEATURES
EXAMPLE-BASED CLASSIFICATION OF PROTEIN SUBCELLULAR LOCATIONS USING PENTA-GRAM FEATURES Jinsuk Kim 1, Ho-Eun Park 2, Mi-Nyeong Hwang 1, Hyeon S. Son 2,3 * 1 Information Technology Department, Korea Institute
More informationMultiple Choice Review- Eukaryotic Gene Expression
Multiple Choice Review- Eukaryotic Gene Expression 1. Which of the following is the Central Dogma of cell biology? a. DNA Nucleic Acid Protein Amino Acid b. Prokaryote Bacteria - Eukaryote c. Atom Molecule
More informationMachine Learning in Action
Machine Learning in Action Tatyana Goldberg (goldberg@rostlab.org) August 16, 2016 @ Machine Learning in Biology Beijing Genomics Institute in Shenzhen, China June 2014 GenBank 1 173,353,076 DNA sequences
More informationProtein Sorting. By: Jarod, Tyler, and Tu
Protein Sorting By: Jarod, Tyler, and Tu Definition Organizing of proteins Organelles Nucleus Ribosomes Endoplasmic Reticulum Golgi Apparatus/Vesicles How do they know where to go? Amino Acid Sequence
More informationGCD3033:Cell Biology. Transcription
Transcription Transcription: DNA to RNA A) production of complementary strand of DNA B) RNA types C) transcription start/stop signals D) Initiation of eukaryotic gene expression E) transcription factors
More informationSupplementary Information 16
Supplementary Information 16 Cellular Component % of Genes 50 45 40 35 30 25 20 15 10 5 0 human mouse extracellular other membranes plasma membrane cytosol cytoskeleton mitochondrion ER/Golgi translational
More information9/2/17. Molecular and Cellular Biology. 3. The Cell From Genes to Proteins. key processes
Molecular and Cellular Biology Animal Cell ((eukaryotic cell) -----> compare with prokaryotic cell) ENDOPLASMIC RETICULUM (ER) Rough ER Smooth ER Flagellum Nuclear envelope Nucleolus NUCLEUS Chromatin
More informationSVM Kernel Optimization: An Example in Yeast Protein Subcellular Localization Prediction
SVM Kernel Optimization: An Example in Yeast Protein Subcellular Localization Prediction Ṭaráz E. Buck Computational Biology Program tebuck@andrew.cmu.edu Bin Zhang School of Public Policy and Management
More informationChapter 1. DNA is made from the building blocks adenine, guanine, cytosine, and. Answer: d
Chapter 1 1. Matching Questions DNA is made from the building blocks adenine, guanine, cytosine, and. Answer: d 2. Matching Questions : Unbranched polymer that, when folded into its three-dimensional shape,
More informationTransport between cytosol and nucleus
of 60 3 Gated trans Lectures 9-15 MBLG 2071 The n GATED TRANSPORT transport between cytoplasm and nucleus (bidirectional) controlled by the nuclear pore complex active transport for macro molecules e.g.
More informationImproved Prediction of Signal Peptides: SignalP 3.0
doi:10.1016/j.jmb.2004.05.028 J. Mol. Biol. (2004) 340, 783 795 Improved Prediction of Signal Peptides: SignalP 3.0 Jannick Dyrløv Bendtsen 1, Henrik Nielsen 1, Gunnar von Heijne 2 and Søren Brunak 1 *
More informationReading Assignments. A. Genes and the Synthesis of Polypeptides. Lecture Series 7 From DNA to Protein: Genotype to Phenotype
Lecture Series 7 From DNA to Protein: Genotype to Phenotype Reading Assignments Read Chapter 7 From DNA to Protein A. Genes and the Synthesis of Polypeptides Genes are made up of DNA and are expressed
More informationIntro Secondary structure Transmembrane proteins Function End. Last time. Domains Hidden Markov Models
Last time Domains Hidden Markov Models Today Secondary structure Transmembrane proteins Structure prediction NAD-specific glutamate dehydrogenase Hard Easy >P24295 DHE2_CLOSY MSKYVDRVIAEVEKKYADEPEFVQTVEEVL
More informationNewly made RNA is called primary transcript and is modified in three ways before leaving the nucleus:
m Eukaryotic mrna processing Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus: Cap structure a modified guanine base is added to the 5 end. Poly-A tail
More informationSUB-CELLULAR LOCALIZATION PREDICTION USING MACHINE LEARNING APPROACH
SUB-CELLULAR LOCALIZATION PREDICTION USING MACHINE LEARNING APPROACH Ashutosh Kumar Singh 1, S S Sahu 2, Ankita Mishra 3 1,2,3 Birla Institute of Technology, Mesra, Ranchi Email: 1 ashutosh.4kumar.4singh@gmail.com,
More informationToday. Last time. Secondary structure Transmembrane proteins. Domains Hidden Markov Models. Structure prediction. Secondary structure
Last time Today Domains Hidden Markov Models Structure prediction NAD-specific glutamate dehydrogenase Hard Easy >P24295 DHE2_CLOSY MSKYVDRVIAEVEKKYADEPEFVQTVEEVL SSLGPVVDAHPEYEEVALLERMVIPERVIE FRVPWEDDNGKVHVNTGYRVQFNGAIGPYK
More informationTutorial 4 Protein Biochemistry 2 Genes to proteins: Protein synthesis, transport, targeting, and degradation
IPAM Cells and Materials: At the Interface between Mathematics, Biology and Engineering Tutorial 4 Protein Biochemistry 2 Genes to proteins: Protein synthesis, transport, targeting, and degradation Dr.
More informationMolecular Biology (9)
Molecular Biology (9) Translation Mamoun Ahram, PhD Second semester, 2017-2018 1 Resources This lecture Cooper, Ch. 8 (297-319) 2 General information Protein synthesis involves interactions between three
More informationOld FINAL EXAM BIO409/509 NAME. Please number your answers and write them on the attached, lined paper.
Old FINAL EXAM BIO409/509 NAME Please number your answers and write them on the attached, lined paper. Gene expression can be regulated at several steps. Describe one example for each of the following:
More informationBiological Process Term Enrichment
Biological Process Term Enrichment cellular protein localization cellular macromolecule localization intracellular protein transport intracellular transport generation of precursor metabolites and energy
More informationThe Discovery of Cells
The Discovery of Cells Microscope observations! General Cell & Organelle Discovery 1600s Observations made by scientists using more powerful microscopes in the 1800s led to the formation of the cell theory.
More informationThe neuron as a secretory cell
The neuron as a secretory cell EXOCYTOSIS ENDOCYTOSIS The secretory pathway. Transport and sorting of proteins in the secretory pathway occur as they pass through the Golgi complex before reaching the
More informationComponents of a functional cell. Boundary-membrane Cytoplasm: Cytosol (soluble components) & particulates DNA-information Ribosomes-protein synthesis
Cell (Outline) - Components of a functional cell - Major Events in the History of Earth: abiotic and biotic phases; anaerobic and aerobic atmosphere - Prokaryotic cells impact on the biosphere - Origin
More informationS1 Gene ontology (GO) analysis of the network alignment results
1 Supplementary Material for Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model Hyundoo Jeong 1, Xiaoning Qian 1 and
More information-14. -Abdulrahman Al-Hanbali. -Shahd Alqudah. -Dr Ma mon Ahram. 1 P a g e
-14 -Abdulrahman Al-Hanbali -Shahd Alqudah -Dr Ma mon Ahram 1 P a g e In this lecture we will talk about the last stage in the synthesis of proteins from DNA which is translation. Translation is the process
More informationUsing AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins
Mol Divers (2008) 12:41 45 DOI 10.1007/s11030-008-9073-0 FULL LENGTH PAPER Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins Bing Niu Yu-Huan Jin Kai-Yan
More informationCHAPTER 9 PROTEIN SUBCELLULAR LOCALIZATION PREDICTION
CHAPTER 9 PROTEIN SUBCELLULAR LOCALIZATION PREDICTION Paul Horton National Institute of Industrial Science and Technology horton-p@aist.go.jp Yuri Mukai National Institute of Industrial Science and Technology
More informationCellular Neuroanatomy I The Prototypical Neuron: Soma. Reading: BCP Chapter 2
Cellular Neuroanatomy I The Prototypical Neuron: Soma Reading: BCP Chapter 2 Functional Unit of the Nervous System The functional unit of the nervous system is the neuron. Neurons are cells specialized
More informationProtein Synthesis. Unit 6 Goal: Students will be able to describe the processes of transcription and translation.
Protein Synthesis Unit 6 Goal: Students will be able to describe the processes of transcription and translation. Types of RNA Messenger RNA (mrna) makes a copy of DNA, carries instructions for making proteins,
More informationUNIT 3 CP BIOLOGY: Cell Structure
UNIT 3 CP BIOLOGY: Cell Structure Page CP: CHAPTER 3, Sections 1-3; HN: CHAPTER 7, Sections 1-2 Standard B-2: The student will demonstrate an understanding of the structure and function of cells and their
More information122-Biology Guide-5thPass 12/06/14. Topic 1 An overview of the topic
Topic 1 http://bioichiban.blogspot.com Cellular Functions 1.1 The eukaryotic cell* An overview of the topic Key idea 1: Cell Organelles Key idea 2: Plasma Membrane Key idea 3: Transport Across Membrane
More informationIdentifying Extracellular Plant Proteins Based on Frequent Subsequences
Identifying Extracellular Plant Proteins Based on Frequent Subsequences Yang Wang, Osmar R. Zaïane, Randy Goebel and Gregory Taylor University of Alberta {wyang, zaiane, goebel}@cs.ualberta.ca Abstract
More informationBME 5742 Biosystems Modeling and Control
BME 5742 Biosystems Modeling and Control Lecture 24 Unregulated Gene Expression Model Dr. Zvi Roth (FAU) 1 The genetic material inside a cell, encoded in its DNA, governs the response of a cell to various
More informationBiology. 7-2 Eukaryotic Cell Structure 10/29/2013. Eukaryotic Cell Structures
Biology Biology 1of 49 2of 49 Eukaryotic Cell Structures Eukaryotic Cell Structures Structures within a eukaryotic cell that perform important cellular functions are known as organelles. Cell biologists
More informationSupplementary Materials for R3P-Loc Web-server
Supplementary Materials for R3P-Loc Web-server Shibiao Wan and Man-Wai Mak email: shibiao.wan@connect.polyu.hk, enmwmak@polyu.edu.hk June 2014 Back to R3P-Loc Server Contents 1 Introduction to R3P-Loc
More informationCell (Learning Objectives)
Cell (Learning Objectives) 1. Understand & describe the basic components necessary for a functional cell. 2. Review the order of appearance of cells on earth and explain the endosymbiotic theory. 3. Compare
More informationEfficient Classification of Multi-label and Imbalanced Data Using Min-Max Modular Classifiers
2006 International Joint Conference on Neural Networks Sheraton Vancouver Wall Centre Hotel, Vancouver, BC, Canada July 16-21, 2006 Efficient Classification of Multi-label and Imbalanced Data Using Min-Max
More informationSupplementary Materials for mplr-loc Web-server
Supplementary Materials for mplr-loc Web-server Shibiao Wan and Man-Wai Mak email: shibiao.wan@connect.polyu.hk, enmwmak@polyu.edu.hk June 2014 Back to mplr-loc Server Contents 1 Introduction to mplr-loc
More information~~~ ~ Nobel Prize in Physiology or Medicine Utpal Tatu
Nobel Prize in Physiology or Medicine 1999 Utpal Tatu The Nobel Prize in Physiology and Medicine for the year 1999 has been awarded to Gunter Blobel for his discovery of signals that direct proteins to
More informationCell Biology Review. The key components of cells that concern us are as follows: 1. Nucleus
Cell Biology Review Development involves the collective behavior and activities of cells, working together in a coordinated manner to construct an organism. As such, the regulation of development is intimately
More informationProtein Synthesis. Unit 6 Goal: Students will be able to describe the processes of transcription and translation.
Protein Synthesis Unit 6 Goal: Students will be able to describe the processes of transcription and translation. Protein Synthesis: Protein synthesis uses the information in genes to make proteins. 2 Steps
More informationTurns sunlight, water & carbon dioxide (CO 2 ) into sugar & oxygen through photosynthesis
CELL PART/ ORGANELLE FUNCTION (what it does) PICTURE Plant, Animal, or Both Cell Membrane controls what goes in & out of the cell protects the cell Nucleus directs all the cell s activities contains cell
More informationSupport vector machine approach for protein subcellular localization prediction. Sujun Hua and Zhirong Sun
BIOINFORMATICS Vol. 17 no. 8 2001 Pages 721 728 Support vector machine approach for protein subcellular localization prediction Sujun Hua and Zhirong Sun Institute of Bioinformatics, State Key Laboratory
More informationCells & Cell Organelles. Doing Life s Work
Cells & Cell Organelles Doing Life s Work Types of cells bacteria cells Prokaryote Eukaryotes animal cells plant cells Cell size comparison Animal cell Bacterial cell most bacteria 1-10 microns eukaryotic
More informationDegeneracy. Two types of degeneracy:
Degeneracy The occurrence of more than one codon for an amino acid (AA). Most differ in only the 3 rd (3 ) base, with the 1 st and 2 nd being most important for distinguishing the AA. Two types of degeneracy:
More informationNucleus. The nucleus is a membrane bound organelle that store, protect and express most of the genetic information(dna) found in the cell.
Nucleus The nucleus is a membrane bound organelle that store, protect and express most of the genetic information(dna) found in the cell. Since regulation of gene expression takes place in the nucleus,
More informationUsing N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization
Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization Annette Höglund, Pierre Dönnes, Torsten Blum, Hans-Werner Adolph, and Oliver
More informationHow do cell structures enable a cell to carry out basic life processes? Eukaryotic cells can be divided into two parts:
Essential Question How do cell structures enable a cell to carry out basic life processes? Cell Organization Eukaryotic cells can be divided into two parts: 1. Nucleus 2. Cytoplasm-the portion of the cell
More information7-2 Eukaryotic Cell Structure
1 of 49 Comparing the Cell to a Factory Eukaryotic Cell Structures Structures within a eukaryotic cell that perform important cellular functions are known as organelles. Cell biologists divide the eukaryotic
More informationCellular Transport. 1. Transport to and across the membrane 1a. Transport of small molecules and ions 1b. Transport of proteins
Transport Processes Cellular Transport 1. Transport to and across the membrane 1a. Transport of small molecules and ions 1b. Transport of proteins 2. Vesicular transport 3. Transport through the nuclear
More informationIncorporating cellular sorting structure for better prediction of protein subcellular locations
Journal of Experimental & Theoretical Artificial Intelligence ISSN: 952-83X (Print) 362-379 (Online) Journal homepage: http://www.tandfonline.com/loi/teta2 Incorporating cellular sorting structure for
More informationCELL PART Expanded Definition Cell Structure Illustration Function Summary Location ALL CELLS DNA Common in Animals Uncommon in Plants Lysosome
CELL PART Expanded Definition Cell Structure Illustration Function Summary Location is the material that contains the Carry genetic ALL CELLS information that determines material inherited characteristics.
More informationFrom Gene to Protein
From Gene to Protein Gene Expression Process by which DNA directs the synthesis of a protein 2 stages transcription translation All organisms One gene one protein 1. Transcription of DNA Gene Composed
More informationProtein Sorting, Intracellular Trafficking, and Vesicular Transport
Protein Sorting, Intracellular Trafficking, and Vesicular Transport Noemi Polgar, Ph.D. Department of Anatomy, Biochemistry and Physiology Email: polgar@hawaii.edu Phone: 692-1422 Outline Part 1- Trafficking
More informationFrom the Bioinformatics Centre, Institute of Microbial Technology, Sector 39A, Chandigarh, India
THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 280, No.??, Issue of??????, pp. 1 xxx, 2005 2005 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. AQ: A Support Vector Machine-based
More informationDiscriminative Motif Finding for Predicting Protein Subcellular Localization
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 1 Discriminative Motif Finding for Predicting Protein Subcellular Localization Tien-ho Lin, Robert F. Murphy, Senior Member, IEEE, and
More informationChapter
Chapter 17 17.4-17.6 Molecular Components of Translation A cell interprets a genetic message and builds a polypeptide The message is a series of codons on mrna The interpreter is called transfer (trna)
More informationClass Work 31. Describe the function of the Golgi apparatus? 32. How do proteins travel from the E.R. to the Golgi apparatus? 33. After proteins are m
Eukaryotes Class Work 1. What does the word eukaryote mean? 2. What is the one major difference between eukaryotes and prokaryotes? 3. List the different kingdoms of the eukaryote domain in the order in
More informationSubcellular Localization of Proteins
Available online at www.scholarsresearchlibrary.com Scholars research library Archives of Applied Science Research, 2011, 3 (6):392-401 (http://scholarsresearchlibrary.com/archive.html) ISSN 0975-508X
More information2011 The Simple Homeschool Simple Days Unit Studies Cells
1 We have a full line of high school biology units and courses at CurrClick and as online courses! Subscribe to our interactive unit study classroom and make science fun and exciting! 2 A cell is a small
More informationCells. Structural and functional units of living organisms
Cells Structural and functional units of living organisms Eukaryotic ( true nucleus ) vs. Prokaryotic ( before nucleus ) cells Proks Eukaryotic ( true nucleus ) vs. Prokaryotic ( before nucleus ) cells
More informationLearning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs Tien-ho Lin CMU-0-02 Language Technologies Institute School of Computer Science Carnegie Mellon University 5000 Forbes
More informationPredicting protein subcellular localisation from amino acid sequence information Olof Emanuelsson Date received (in revised form): 10th September 2002
Olof Emanuelsson works in close collaboration with Gunnar von Heijne on developing methods for predicting subcellular localisation of proteins. He is at the Stockholm Bioinformatics Center (SBC), a joint
More informationWhat Kind Of Molecules Carry Protein Assembly Instructions From The Nucleus To The Cytoplasm
What Kind Of Molecules Carry Protein Assembly Instructions From The Nucleus To The Cytoplasm What kind of reaction produces large molecules by linking small molecules? molecules carry protein assembly
More informationStatistical Machine Learning Methods for Bioinformatics IV. Neural Network & Deep Learning Applications in Bioinformatics
Statistical Machine Learning Methods for Bioinformatics IV. Neural Network & Deep Learning Applications in Bioinformatics Jianlin Cheng, PhD Department of Computer Science University of Missouri, Columbia
More informationSequence Alignment Techniques and Their Uses
Sequence Alignment Techniques and Their Uses Sarah Fiorentino Since rapid sequencing technology and whole genomes sequencing, the amount of sequence information has grown exponentially. With all of this
More informationCell Organelles Tutorial
1 Name: Cell Organelles Tutorial TEK 7.12D: Differentiate between structure and function in plant and animal cell organelles, including cell membrane, cell wall, nucleus, cytoplasm, mitochondrion, chloroplast,
More informationMean Hes score. Threshold
Mean Hes score 0.1 0.09 Common 0.08 Family 0.07 0.06 0.05 0.04 0.03 0.02 0.01 0 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 Threshold SUPPLEMENTARY FIG. 1. Trend of mean Hes scores calculated based on the
More informationWhy Bother? Predicting the Cellular Localization Sites of Proteins Using Bayesian Model Averaging. Yetian Chen
Predicting the Cellular Localization Sites of Proteins Using Bayesian Model Averaging Yetian Chen 04-27-2010 Why Bother? 2008 Nobel Prize in Chemistry Roger Tsien Osamu Shimomura Martin Chalfie Green Fluorescent
More informationSyllabus of BIOINF 528 (2017 Fall, Bioinformatics Program)
Syllabus of BIOINF 528 (2017 Fall, Bioinformatics Program) Course Name: Structural Bioinformatics Course Description: Instructor: This course introduces fundamental concepts and methods for structural
More informationJEPSLD: A JUDGMENTAL EUKARYOTIC PROTEIN SUBCELLULAR LOCATION DATABASE. Sanjeev Patra
JEPSLD: A JUDGMENTAL EUKARYOTIC PROTEIN SUBCELLULAR LOCATION DATABASE by Sanjeev Patra A thesis submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the
More informationSequence analysis and comparison
The aim with sequence identification: Sequence analysis and comparison Marjolein Thunnissen Lund September 2012 Is there any known protein sequence that is homologous to mine? Are there any other species
More informationA NEURAL NETWORK METHOD FOR IDENTIFICATION OF PROKARYOTIC AND EUKARYOTIC SIGNAL PEPTIDES AND PREDICTION OF THEIR CLEAVAGE SITES
International Journal of Neural Systems, Vol. 8, Nos. 5 & 6 (October/December, 1997) 581 599 c World Scientific Publishing Company A NEURAL NETWORK METHOD FOR IDENTIFICATION OF PROKARYOTIC AND EUKARYOTIC
More informationEukaryotic vs. Prokaryotic genes
BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 18: Eukaryotic genes http://compbio.uchsc.edu/hunter/bio5099 Larry.Hunter@uchsc.edu Eukaryotic vs. Prokaryotic genes Like in prokaryotes,
More informationOverview of Cells. Prokaryotes vs Eukaryotes The Cell Organelles The Endosymbiotic Theory
Overview of Cells Prokaryotes vs Eukaryotes The Cell Organelles The Endosymbiotic Theory Prokaryotic Cells Archaea Bacteria Come in many different shapes and sizes.5 µm 2 µm, up to 60 µm long Have large
More informationAS Biology Summer Work 2015
AS Biology Summer Work 2015 You will be following the OCR Biology A course and in preparation for this you are required to do the following for September 2015: Activity to complete Date done Purchased
More informationPrediction of signal peptides and signal anchors by a hidden Markov model
In J. Glasgow et al., eds., Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, 122-13. AAAI Press, 1998. 1 Prediction of signal peptides and signal anchors by a hidden Markov model Henrik
More informationTHE CELL 3/15/15 HUMAN ANATOMY AND PHYSIOLOGY I THE CELLULAR BASIS OF LIFE
HUMAN ANATOMY AND PHYSIOLOGY I Lecture: M 6-9:30 Randall Visitor Center Lab: W 6-9:30 Swatek Anatomy Center, Centennial Complex Required Text: Marieb 9 th edition Dr. Trevor Lohman DPT (949) 246-5357 tlohman@llu.edu
More informationAnalysis and visualization of protein-protein interactions. Olga Vitek Assistant Professor Statistics and Computer Science
1 Analysis and visualization of protein-protein interactions Olga Vitek Assistant Professor Statistics and Computer Science 2 Outline 1. Protein-protein interactions 2. Using graph structures to study
More informationGeneral A&P Cell Labs - Cellular Anatomy & Division (Mitosis) Pre-Lab Guide
1 General A&P Cell Labs - Cellular Anatomy & Division (Mitosis) Pre-Lab AWalk-About@ Guide Have someone in your group read the following out loud, while the others read along: In this "Walk About", we
More informationChapter 4. Table of Contents. Section 1 The History of Cell Biology. Section 2 Introduction to Cells. Section 3 Cell Organelles and Features
Cell Structure and Function Table of Contents Section 1 The History of Cell Biology Section 2 Introduction to Cells Section 3 Cell Organelles and Features Section 4 Unique Features of Plant Cells Section
More informationBiology. Mrs. Michaelsen. Types of cells. Cells & Cell Organelles. Cell size comparison. The Cell. Doing Life s Work. Hooke first viewed cork 1600 s
Types of cells bacteria cells Prokaryote - no organelles Cells & Cell Organelles Doing Life s Work Eukaryotes - organelles animal cells plant cells Cell size comparison Animal cell Bacterial cell most
More informationAnalysis of N-terminal Acetylation data with Kernel-Based Clustering
Analysis of N-terminal Acetylation data with Kernel-Based Clustering Ying Liu Department of Computational Biology, School of Medicine University of Pittsburgh yil43@pitt.edu 1 Introduction N-terminal acetylation
More informationA Bayesian System Integrating Expression Data with Sequence Patterns for Localizing Proteins: Comprehensive Application to the Yeast Genome
A Bayesian System Integrating Expression Data with Sequence Patterns for Localizing Proteins: Comprehensive Application to the Yeast Genome Amar Drawid 1 & Mark Gerstein 1,2 * Departments of (1) Molecular
More informationIMPORTANCE OF SECONDARY STRUCTURE ELEMENTS FOR PREDICTION OF GO ANNOTATIONS
IMPORTANCE OF SECONDARY STRUCTURE ELEMENTS FOR PREDICTION OF GO ANNOTATIONS Aslı Filiz 1, Eser Aygün 2, Özlem Keskin 3 and Zehra Cataltepe 2 1 Informatics Institute and 2 Computer Engineering Department,
More informationChapter 7.2. Cell Structure
Chapter 7.2 Cell Structure Daily Objectives Describe the structure and function of the cell nucleus. Describe the function and structure of membrane bound organelles found within the cell. Describe the
More informationln vited Revie w Prohormone and proneuropeptide synthesis and secretion Histology and Histopathology
Histol Histopathol (1 997) 12: 1 179-1 188 Histology and Histopathology ln vited Revie w Prohormone and proneuropeptide synthesis and secretion M.J. Perone and M.G. Castro Molecular Medicine Unit, Department
More informationPROTEIN SUBCELLULAR LOCALIZATION PREDICTION BASED ON COMPARTMENT-SPECIFIC BIOLOGICAL FEATURES
3251 PROTEIN SUBCELLULAR LOCALIZATION PREDICTION BASED ON COMPARTMENT-SPECIFIC BIOLOGICAL FEATURES Chia-Yu Su 1,2, Allan Lo 1,3, Hua-Sheng Chiu 4, Ting-Yi Sung 4, Wen-Lian Hsu 4,* 1 Bioinformatics Program,
More informationCell Types. Prokaryotes
Cell Types Prokaryotes before nucleus no membrane-bound nucleus only organelle present is the ribosome all other reactions occur in the cytoplasm not very efficient Ex.: bacteria 1 Cell Types Eukaryotes
More informationCAP 5510 Lecture 3 Protein Structures
CAP 5510 Lecture 3 Protein Structures Su-Shing Chen Bioinformatics CISE 8/19/2005 Su-Shing Chen, CISE 1 Protein Conformation 8/19/2005 Su-Shing Chen, CISE 2 Protein Conformational Structures Hydrophobicity
More information