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Introduction to Bioinformatics Lecture 1: Overview of Bioinformatics and Molecular BiologyWhat is Bioinformatics? Defining the terms bioinformatics and computational biology is not necessarily aneasy task, as evidenced by multiple definitions available over the web. A recentgoogle search for "definition of bioinformatics" returned over 43,000 results! Inthe past few years, as the areas have grown, a greater confusion into these twoterms has prevailed. For some, the terms bioinformatics and computationalbiology have become completely interchangeable terms, while for others, there isa great distinction. I'll throw my two cents in, based on what my experience hasbeen to the consensus use of these two terms.Computational biology and bioinformatics are multidisciplinary fields, involvingresearchers from different areas of specialty, including (but in no means limitedto) statistics, computer science, physics, biochemestry, genetics, molecular biology and mathematics. The goal of these two fields is as follows: Bioinformatics: Typically refers to the field concerned with the collectionand storage of biological information. All matters concerned with biologicaldatabases are considered bioinformatics. Computational biology: Refers to the aspect of developing algorithmsand statistical models necessary to analyze biological data through the aidof computers.In this respect, my understanding of bioinformatics and computational biologyfollows the NIH definitions listed below: Bioinformatics: Research, development, or application of computational tools and approachesfor expanding the use of biological, medical, behavioral or health data, including those to acquire,store, organize, archive, analyze, or visualize such data. Computational Biology: The development and application of data-analytical and theoreticalmethods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. Others have offered various opinions into these definitions as well:http://kbrin.kwing.louisville.edu/~rouchka/definition.html Image Source: http://ccb.wustl.edu/ Bioinformatics = Hot Field Smart Money: #1 among next hot jobs http://smartmoney.com/consumer/index.cfm?story=working-june02 Business Week: Among 50 Masters of Innovation http://www.businessweek.com/bw50/content/mar2001/bf20010323_198.htm So why is bioinformatics a hot field? One answer to this question is that it is tied to thehuman genome project which has generated a lot of popular interest. Various advancesin molecular biology techniques (such as genome sequencing and microarrays) has led toa large amount of data that needs to be analyzed. Now that we are close to having thehuman genome finished, what does it all mean? Thats where bioinformatics steps in.Bioinformatics can lead to important discoveries as well as help companies save time andmoney in the long run. In addition, there needs to be methods to manage large amountsof data. One of the biggest reasons for bioinformatics being a hot field is the old supplyand demand

adage. There just are too few people adequately trained in both biology andcomputer science to solve the problems that biologists need to have solved. Introduction to Molecular Biology (For a good overview of this topic, please read:http://www.ebi.ac.uk/microarray/biology_intro.html )In order to be a good computational biologist, it is important to understand theterminology and basic processes behind the biological problems. Many interesting problems arise out of sequence analysis. There are two different types of biologicalsequences studied in this class: DNA/RNA and amino acids. But first, lets make surethe basics are covered. Cells Every organism is made up of tiny structures called cells. Often these cells are too smallto be seen with the naked eye. Each cell is in itself a complex system enclosed in amembrane. Some organisms, such as bacteria and bakers yeast are composed of only asingle cell (i.e. they are unicellular). Other organisms are made up of many differentcells (i.e. they are multicellular). For instance, the human body is composed of around 60trillion cells. Humans have about 320 different cell types, each having a different type of function or structural property. Structure of an animal cell. Image source: www.ebi.ac.uk/microarray/ biology_intro.htm There are two types of organisms: eukaryotes and prokaryotes. Eukaryotes (or as BruceRoe from the University of Oklahoma calls them the You and I Karyotes) representmost of the organisms which we can see, including plants and animals. Prokaryotes (such as bacteria) are smaller than eukaryotic cells and have simpler structure.Prokaryotes are single cellular organisms (but not all single-celled organisms are prokaryotes!)So what is the difference between the two types of cells? A eukaryotic cell has a nucleus,which is separated from the rest of the cell by a membrane. Inside the nucleus are thechromosomes, where all of the genetic information for the organism is stored. Inaddition, eukaryotic cells contain membrane bound organelles with various functions,including centrioles, lysosomes, mitochondria, ribosomes, etc.Contained within the nucleus are one or several long double stranded DNA moleculesorganized as chromosomes. For humans, there are 22 pairs of autosomes, as well as one pair of sex chromosomes. One copy of each pair is inherited from each parent. Karyotype showing the 23 pairs of human chromosomes. Image source: http://avery.rutgers.edu/WSSP/StudentScholars/Session8/Session8.html Image source: www.biotec.or.th/Genome/ whatGenome.html DNA Deoxyribonucleic Acid (DNA) is the basis for the building blocks encoding theinformation of life. A single stranded DNA molecule, called a polynucleotide or oligomer , is a chain of small molecules called nucleotides. There are four differentnucleotides, or bases: adenosine (A), cytosine (C), guanine (G)

and thymine (T).The bases can be separated into two different types: purines (A and G) and pyrimidines(C and T). The difference between purines and pyrimidines is in the base structure.Stringing together a simple alphabet of four characters together we can get enoughinformation to create a complex organism! Different nucleotides can be strung together to form a polynucleotide. However, the ends of the polynucleotide are different, meaningthat each polynucleotide sequence will have a directionality. The ends of the polynucleotide are marked either 3 or 5. The general convention is to label the codingstrand from 5 to 3 (left to right). For instance, the following is a polynucleotide: 5 G T A A A G T C C C G T T A G C3 DNA can be either single-stranded or double stranded. When DNA is double-stranded,the second strand is referred to as the reverse complement strand. This name is derivedfrom the fact that the directionality of this second strand runs in the opposite direction asthe first, and the fact that the bases in the second strand are complementary to the bases inthe first. Complementary bases are determined by which pairs of nucleotides can form bonds between them. In the case of DNA, A binds to T, and C binds to G. For the polynucleotide given above, the double-stranded polynucleotide is as follows: 5 G T

A A A G T C C C G T T A G C3 | | | | | | | | | | | | | | | | 3C A T T T C A G G G C A A T C G5

Two complementary polynucleotide chains form a stable structure known as the DNAdouble helix. This spring represents the 50 th anniversary of the discovery of the doublehelix structure of DNA by Watson, Crick and Franklin. DNA double helix structure .Image source: www.genecrc.org/site/ lc/lc2b.htm Note that in this image, there appear to be two types of grooves: A larger one, which iscalled the major groove and a smaller one, known as the minor groove. In addition, thereare roughly 10.5 base pairs in one complete turn of the helix. RNA Ribonucleic Acid (RNA) is similar to DNA in the fact that it is constructed fromnucleotides. However, instead of thymine (T), an alternative base uracil (U) is found inRNA. RNA can be found as double-stranded or single-stranded, and can also be part of ahybrid helix where one strand is an RNA strand and the other is a DNA strand. RNA isgenerally found as a single stranded molecule that may form a secondary structure or tertiary structures due to the complementary bases between parts of the same strand.RNA folding will be discussed in detail during a later class period. RNA is important in of 232 Leave a Comment Comment must not be empty. You must be logged in <http://www.scribd.com/login> to leave a comment. Submit Characters: 400 <http://www.scribd.com/santosh_divya_1> Santosh Divya <http://www.scribd.com/santosh_divya_1> nice reply03 / 20 / 2012 <http://www.scribd.com/events/2017032187?user_id=133485705-santosh-divya> <http://www.scribd.com/shantiabrookie> shantiabrookie <http://www.scribd.com/shantiabrookie> very nice reply03 / 12 / 2012 <http://www.scribd.com/events/2007659594?user_id=9073643-shantiabrookie> <http://www.scribd.com/econ_nutsugah> Emmanuel Con-Nutsugah <http://www.scribd.com/econ_nutsugah> thnx bt i can seem to download this file reply01 / 14 / 2012 <http://www.scribd.com/events/1957562197?user_id=112345244-emmanuel-con-nutsugah > <http://www.scribd.com/uherou> Uwizeye Herou <http://www.scribd.com/uherou> nice book reply06 / 09 / 2011

<http://www.scribd.com/events/260580205?user_id=79979870-uwizeye-herou> <http://www.scribd.com/marmiw> Marmi Nancy Wei <http://www.scribd.com/marmiw> Thank you very much!! reply05 / 23 / 2011 <http://www.scribd.com/events/242625613?user_id=76377581-marmi-nancy-wei> <http://www.scribd.com/jminesh> Minesh Jethva <http://www.scribd.com/jminesh> thanx for share reply03 / 11 / 2011 <http://www.scribd.com/events/178037124?user_id=40240272-minesh-jethva> <http://www.scribd.com/rajesh_sahu_1> Rajesh Kumar Sahu <http://www.scribd.com/rajesh_sahu_1> bio informatics reply05 / 24 / 2010 <http://www.scribd.com/events/31740222?user_id=27989511-rajesh-kumar-sahu> <http://www.scribd.com/naveenbt> naveenbt <http://www.scribd.com/naveenbt> this is very usefull thanks a lot reply12 / 24 / 2009 <http://www.scribd.com/events/20687676?user_id=20788707-naveenbt> Show More Comment must not be empty. You must be logged in <http://www.scribd.com/login> to leave a comment. Submit Characters: ... complete notes on Bioinformatics this is a pdf document with complete notes on bioinformatics for students. Download or Print /54,540 Reads/ Info and Rating Category: /Uncategorized./ Rating: (55 Ratings) Upload Date: 03/25/2007 Copyright: Attribution Non-commercial Tags: bioinformatics <http://www.scribd.com/tag/bioinformatics?l=1> Science-Biology <http://www.scribd.com/tag/Science-Biology?l=1> bioinformatics <http://www.scribd.com/tag/bioinformatics?l=1> Science-Biology <http://www.scribd.com/tag/Science-Biology?l=1> (fewer <#>) Flag document for inapproriate content This is a private document. </static/help?type=private> <http://www.scribd.com/pablasarabjot> Uploaded by pablasarabjot <http://www.scribd.com/pablasarabjot>

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