Welcome to Chem 434 Bioinformatics Sept 20, 2012 Review of course prerequisites Review of syllabus Review of CSULA Bioinformatics Course website.

Slides:



Advertisements
Similar presentations
Introduction to Bioinformatics. What is Bioinformatics Easy Answer Using computers to solve molecular biology problems; Intersection of molecular biology.
Advertisements

BIOINFORMATICS Ency Lee.
Bioinformatics What is bioinformatics? Why bioinformatics? The major molecular biology facts Brief history of bioinformatics Typical problems of bioinformatics:
Bioinformatics at IU - Ketan Mane. Bioinformatics at IU What is Bioinformatics? Bioinformatics is the study of the inherent structure of biological information.
. Class 1: Introduction. The Tree of Life Source: Alberts et al.
Introduction to Bioinformatics Spring 2008 Yana Kortsarts, Computer Science Department Bob Morris, Biology Department.
Using Bioinformatics to Make the Bio- Math Connection The Confessions of a Biology Teacher.
Bioinformatics: a Multidisciplinary Challenge Ron Y. Pinter Dept. of Computer Science Technion March 12, 2003.
R ICHARD M ANNING K ARP. R ICHARD M. K ARP Computer scientist and computational theorist Born: o January 3, 1935 (age 76) o Boston, Massachusetts Attended.
Introduction to Genomics, Bioinformatics & Proteomics Brian Rybarczyk, PhD PMABS Department of Biology University of North Carolina Chapel Hill.
Welcome to Chem 434 Bioinformatics March 25, 2008 Review of course prerequisites Review of syllabus Review of Bioinformatics Course website Course objectives.
Welcome to Chem 434 Bioinformatics March 29, 2005 Review of course prerequisites Course objectives Become proficient at using existing bioinformatics.
Integration of Bioinformatics into Inquiry Based Learning by Kathleen Gabric.
Course Summary June 2, 2005 Programming Workshop Overview of course (presentation) Protein modeling, part 2 Instructor evaluations.
Bioinformatics Student host Chris Johnston Speaker Dr Kate McCain.
Recap Sometimes it is necessary to conduct Bad Science – often the product of having too much information Human Genome Project changed natural scientists.
Bioinformatics in the Biology Curriculum Gloria Rendon NCSA July 2008.
Phylogenetic Shadowing Daniel L. Ong. March 9, 2005RUGS, UC Berkeley2 Abstract The human genome contains about 3 billion base pairs! Algorithms to analyze.
Sequence Analysis. Today How to retrieve a DNA sequence? How to search for other related DNA sequences? How to search for its protein sequence? How to.
Bioinformatics Unit 1: Data Bases and Alignments Lecture 3: “Homology” Searches and Sequence Alignments (cont.) The Mechanics of Alignments.
Signaling Pathways and Summary June 30, 2005 Signaling lecture Course summary Tomorrow Next Week Friday, 7/8/05 Morning presentation of writing assignments.
Bioinformatics Original definition (1979 by Paulien Hogeweg): “application of information technology and computer science to the field of molecular biology”
Chromosomes carry genetic information
Welcome to Introduction to Bioinformatics Computing aka BIC1.
Arabidopsis Gene Project GK-12 April Workshop Karolyn Giang and Dr. Mulligan.
Sequence Analysis Determining how similar 2 (or more) gene/protein sequences are (too each other) is a “staple” function in bioinformatics. This information.
Lesson 10 Bioinformatics
Bioinformatics.
C OMPUTATIONAL BIOLOGY. O UTLINE Proteins DNA RNA Genetics and evolution The Sequence Matching Problem RNA Sequence Matching Complexity of the Algorithms.
1 Bio + Informatics AAACTGCTGACCGGTAACTGAGGCCTGCCTGCAATTGCTTAACTTGGC An Overview پرتال پرتال بيوانفورماتيك ايرانيان.
CSE 6406: Bioinformatics Algorithms. Course Outline
Protein Sequence Alignment and Database Searching.
Welcome to Introduction to Bioinformatics Computing aka BIC1.
A brief Introduction to Bioinformatics Y. SINGH NELSON R. MANDELA SCHOOL OF MEDICINE DEPARTMENT OF TELEHEALTH Content licensed under.
Introduction to Bioinformatics Spring 2002 Adapted from Irit Orr Course at WIS.
BIOINFORMATICS IN BIOCHEMISTRY Bioinformatics– a field at the interface of molecular biology, computer science, and mathematics Bioinformatics focuses.
Introduction to Bioinformatics Yana Kortsarts References: An Introduction to Bioinformatics Algorithms bioalgorithms.info.
What is Genetic Research?. Genetic Research Deals with Inherited Traits DNA Isolation Use bioinformatics to Research differences in DNA Genetic researchers.
CSCI 6900/4900 Special Topics in Computer Science Automata and Formal Grammars for Bioinformatics Bioinformatics problems sequence comparison pattern/structure.
Bioinformatics: Theory and Practice – Striking a Balance (a plea for teaching, as well as doing, Bioinformatics) Practice (Molecular Biology) Theory: Central.
Construction of Substitution Matrices
REMINDERS 2 nd Exam on Nov.17 Coverage: Central Dogma of DNA Replication Transcription Translation Cell structure and function Recombinant DNA technology.
Bioinformatics Computing 1 CMP 807 – Day 1 Kevin Galens.
A Tutorial of Sequence Matching in Oracle Haifeng Ji* and Gang Qian** * Oklahoma City Community College ** University of Central Oklahoma.
Overview of Bioinformatics 1 Module Denis Manley..
Introduction to Bioinformatics Dr. Rybarczyk, PhD University of North Carolina-Chapel Hill
BIOLOGICAL DATABASES. BIOLOGICAL DATA Bioinformatics is the science of Storing, Extracting, Organizing, Analyzing, and Interpreting information in biological.
BLAST, which stands for basic local alignment search tool, is a heuristic algorithm that is used to find similar sequences of amino acids or nucleotides.
EB3233 Bioinformatics Introduction to Bioinformatics.
COMPUTATIONAL BIOLOGIST DR. MARTIN TOMPA Place of Employment: University of Washington Type of Work: Develops computer programs and algorithms to identify.
Bioinformatics Lecture to accompany BLAST/ORF finder activity
BLAST, which stands for basic local alignment search tool, is a heuristic algorithm that is used to find similar sequences of amino acids or nucleotides.
Integration of Bioinformatics into Inquiry Based Learning by Kathleen Gabric.
Bioinformatics Chem 434 Dr. Nancy Warter-Perez Computer Engineering Dr. Jamil Momand Chemistry & Biochemistry.
Teaching Bioinformatics Nevena Ackovska Ana Madevska - Bogdanova.
Bioinformatics Dipl. Ing. (FH) Patrick Grossmann
An Introduction to NCBI & BLAST National Center for Biotechnology Information Richard Johnston Pasadena City College.
Biotechnology and Bioinformatics: Bioinformatics Essential Idea: Bioinformatics is the use of computers to analyze sequence data in biological research.
PROTEIN IDENTIFIER IAN ROBERTS JOSEPH INFANTI NICOLE FERRARO.
Prepared By: Syed Khaleelulla Hussaini. Outline Proteins DNA RNA Genetics and evolution The Sequence Matching Problem RNA Sequence Matching Complexity.
Bioinformatics Overview
Research Paper on BioInformatics
Bioinformatics Madina Bazarova. What is Bioinformatics? Bioinformatics is marriage between biology and computer. It is the use of computers for the acquisition,
What is Bioinformatics?
Bioinformatics and BLAST
There are four levels of structure in proteins
Bioinformatics Biological Data Computer Calculations +
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
Bioinformatics Vicki & Joe.
Presentation transcript:

Welcome to Chem 434 Bioinformatics Sept 20, 2012 Review of course prerequisites Review of syllabus Review of CSULA Bioinformatics Course website

Course logistics Course Website ( /Bioinformaticscourse.html) /Bioinformaticscourse.html

Rationale for offering bioinformatics 1. Need to understand how popular bioinformatics algorithms operate (Clustal W, BLAST, PSIPRED). 2. A programming assignment gives a taste of what it is like to be a developer.

Definition of Bioinformatics Use of computers to catalog and organize biological information into meaningful entities.

Learning Outcomes 1) Retrieve gene sequence information from GenBank. 2) Use BLAST to conduct gene similarity searches. 3) Align multiple sequences with Clustal W software. 4) Predict secondary structures with PSIPRED. 5) Display and compare protein structures. 6) Write software programs that perform queries a database with a protein sequence. 7) Understand the theory that led to the development of scoring methods commonly used to measure sequence similarities.

How is Bioinformatics Used? Experimental proof is still the “Gold Standard”. Bioinformatics isn’t going to replace lab work anytime soon Bioinformatics is used to help “focus” the experiments of the benchtop scientist

Useful textbooks on the subject Beginning Python: From Novice to Professional, Apress 2008 ISBN:

Bioinformatics – Why to Do It Richard Karp’s Motivation: "Find genetic basis of complex diseases so that we can develop more effective modes of treatment."

Bioinformatics – How to Do It “… solving biological problems requires far more than clever algorithms: it involves a creative partnership between biologists and mathematical scientists to arrive at an appropriate mathematical model, the acquisition and use of diverse sources of data, and statistical methods to show that the biological patterns and regularities that we discover could not be due to chance." -- Richard Karp

Who is Richard Karp? UC Berkeley Professor Recipient of Turing Award (1985) The Benjamin Franklin Medal in Computer and Cognitive Science (2004) The Kyoto Prize (2008) Turing award citation For his continuing contributions to the theory of algorithms … most notably, contributions to the theory of NP-completeness. Karp introduced the now standard methodology for proving problems to be NP-complete which has led to the identification of many theoretical and practical problems as being computationally difficult.NP-completeness Recent work on transcriptional regulation of genes, discovering conserved regulatory pathways, analyzing genetic variations in humans.

Basis of molecular life sciences Hierarchy of relationships (some exceptions): Genome Gene 1Gene 3Gene 2Gene X Protein 1Protein 2Protein 3Protein X Function 1Function 2Function 3Function X

Structure of a nucleotide within DNA A. B.

The structure of DNA. 5’ACTG 3’TGAC

Table 1.1. Single letter abbreviations used for DNA nucleotide sequences One letter abbreviation Nucleotide nameBase nameCategory AAdenosine monophosphate AdeninePurine CCytidine monophosphate CytosinePyrimidine GGuanosine monophosphate GuaninePurine TThymidine monophosphate ThyminePyrimidine NAny nucleotideAny baseNA RA or G Purine YC or T Pyrimidine -or * Gap human GCTGTCCCTCACTGTTGAATTTTCTCTAACTTCAAGGCCCATATCTGTGAAATGCT drosophila GCTATTAGT--ATCTTAAGTTTGTATTA GTCCTTGTTCGTAAGGCGTT

RNA-the intermediary A. OH B.

Central Dogma of Molecular Biology Reverse transcription

The genetic code

Amino acids-the building blocks of proteins

V L I M F N Q E H K R D G A S T Y W C P

Table 1.2. Abbreviations used for ambiguous and rare amino acids 1-letter abbreviation 3-letter abbreviationMeaning BAsn or AspAsparagine or aspartic acid JXleIsoleucine or leucine OPyrPyrrolysine USecSelenocysteine ZGln or GluGlutamine or glutamic acid XXaaAny amino acid - or *---No corresponding residue (gap)

Levels of protein structure

Levels of protein structure II

Sickle cell anemia

Paper chromatography separation of hemoglobin peptides.