This chapter provides coverage underlying the main principles of both genetic and bioinformatics analysis which should make this book suitable for all students of bioinformatics beginners. The successive parts provide the readers with quick and useful navigation into the world of bioinformatics and its useful tools and techniques. Book importance: This Book is advisable for both researchers and students who want to begin learning about bioinformatics.
In my opinion, this is the book to start with comparing to other hardcore bioinformatics books. Das Erbe der Jedi-Ritter 3. Der Todeskreuzer. The Headspace Guide To The Offer: Liebe mich nicht The Pact: Versprich mir nichts The Play: Spiel nicht mit mir Welche Heilpflanze ist das?
You'll be amazed at all the things you can accomplish just by logging on and following these trusty directions. You get the tools you need to: Analyze all types of sequences Use all types of databases Work with DNA and protein sequences Conduct similarity searches Build a multiple sequence alignment Edit and publish alignments Visualize protein 3-D structures Construct phylogenetic trees This up-to-date second edition includes newly created and popular databases and Internet programs as well as multiple new genomes.
It provides tips for using servers and places to seek resources to find out about what's going on in the bioinformatics world. Bioinformatics For Dummies will show you how to get the most out of your PC and the right Web tools so you'll be searching databases and analyzing sequences like a pro!
Get A Copy. Paperback , pages. Published December 18th by For Dummies first published January 15th More Details Original Title. Other Editions Friend Reviews. To see what your friends thought of this book, please sign up.
To ask other readers questions about Bioinformatics For Dummies , please sign up. Be the first to ask a question about Bioinformatics For Dummies. Lists with This Book. Community Reviews. Trading Chaos 2nd Ed.
Anatomy and Physiology For Dummies 2nd ed. You get the tools you need to:. This up-to-date second edition includes newly created and popular databases and Internet programs as well as multiple new genomes. View Instructor Companion Site. View Student Companion Site. Cedric has used and abused the facilities offered by science to wander around Europe. After a Ph. He then did a post-doc in Lausanne Switzerland with Phillip Bucher, and remained involved with the Swiss Institute of Bioinformatics for several years.
Having had his share of rain, snow, and wind, Cedric has finally settled in Marseilles, where the sun and the sea are simply warmer than any other place he has lived in.
Cedric dedicates most of his research to the multiple sequence alignment problem and its many applications in biology. His friends claim that his entire life past, present, future is somehow stuffed into the T-Coffee multiple-sequence alignment package.
When he is not busy dismantling T-Coffee and brewing new sequences, Cedric enjoys life in the company of his wife, Marita. Request permission to reuse content from this site. For your convenience, we have listed the resources chapter by chapter, following the order in which they appear in the book. Along with the chapters the authors have provided images and diagrams used in the book. You may go to the corresponding chapter to download that specific chapter.
All images are kept in. You may download winzip a utility to open the archives. CAZy, an information resource on enzymes that degrade, modify, or create glycosidic bonds.
For AF, it indicates that the sequence belongs to chromosome 15, and was more precisely mapped on the long arm q of this chromosome, within the q Their purpose is to describe precisely the reconstruction of the various mRNAs spread over several separate entries. Concentrate on the first gene order formula to understand how this works: AF All it says is: 1. Take nucleotides from positions 1 to from entry AF Add nucleotides from positions 1 to from the current entry AF Add nucleotides 1 to 45 from entry AF Add nucleotides to from entry AF Add nucleotides to from the same entry AF Add nucleotides to from the same entry again.
Alternative splicing is a common property of higher eukaryotic gene expression. If you use the same parsing logic as gene order which we describe in the preceding bullet , you can produce the results we summarize in Table See Figure for the sequence of the nuclear form of the protein. Look at AF if you want to see multiple occurrences of the exon field in a single entry.
The sequence section, located in the bottom part of the entry, is format- ted as usual. Refer again to Figure Genomic sequence Understanding how to splice back the various nucleotide sequence fragments to form an mRNA and the associated coding regions from segmented GenBank entries was the main difficulty of this chapter.
Normally you get these accession numbers by reading articles that explicitly mention them when reporting about the corresponding sequence.
There are some monkey sequences as well! The following shows you how you should proceed, step by step: 1. The four last entries indicate the full amino-acid sequence of the two forms nuclear and mitochondrial of the dUTPase protein, as well as the alternative exon usage pattern.
Not a bad start! Click the Links link to the right of the AF entry ID line, and then choose Related Sequences from the pull-down menu that appears. This retrieves a total of 20 entries. Among these entries, some contain mRNA sequences such as U Notice that we restricted the search to the [Title] field here — not as a protein name, which is what we did in Step 3. This illustrates the general difficulty in retrieving all entries relevant to a given subject, due to inconsistent usage of synonymous terms such dUTPase, dUTP pyrophosphatase, or deoxyuridine triphosphatase and fields.
Open the Limits setting menu by clicking the Limits link below the Search window. Select the Exclude ESTs check box. Scroll to the top of the form, and click the Go button. Only eleven GenBank entries survive this particular limit-setting. Feel free to use this handy Search-within-Limits protocol to try other field- restricted searches in GenBank. Making a gene-centered query involves asking a question that relates directly to a specific gene, rather than going through all known pieces of sequences related to that gene.
The main advantage of gene-centric databases is that they return results that are more synthetic than a long list of GenBank entries, and make much more sense to the biologists. Basically, you get the whole story at once.
This resource makes it possible to gather important information related to a genetic locus, a specific place on a chromosome where a given gene has been identified. Thanks to this service, you can rapidly find out everything that is known about your favorite gene, or its genomic surrounding.
From the Search pull-down menu, choose Gene. You get a screen that looks like Figure The Results page you see in Figure is your doorway to a wealth of infor- mation. By clicking the DUT link — or by changing the display option into Full Report — you can now get to a large body of information concerning this par- ticular gene and its genomic environment. The top of the DUT entry see Figure provides a general description of what this gene is all about — and what function its products are known to perform, as well as a large variety of links right-side menu to other data- bases or NCBI files.
Figure displays the next part of the entry: a schematic view of the Human DUT gene structure, with its seven exons used differentially and spread over 11, base pairs of genomic DNA on Chromosome The long entry then continues — additional sections provide information on potential interactions with other gene products, homologous sequences in other organisms, protein functions, and relevant metabolic pathways — as well as a list of all corresponding sequence entries in GenBank.
This one-stop shopping capacity illustrates the useful concept of a gene-centric database. What you have here are all the types of mRNA sequences that have been observed and recorded in GenBank for this gene. You can see that variations mainly involve the two first exons.
These variants alternative transcripts include the mitochondrial and nuclear forms of dUTPase Table Click here for a detailed map and experimental evidence. You can review for yourself the experimental arguments in favor of the various mRNA models presented, right down to the nucleotide level. Working with Whole-Genome Databases The most recent genome-centric databases are the modern bioinformatic response to the proliferation of complete genome sequencing projects.
The goal of these new types of resources is to gather all the information you need on a given organism, clearly separated from all the others, so you can more easily target your analyses on all genes from a specific genome. These new resources also promote comparisons of whole genomes with whole genomes, a new field of endeavor called comparative genomics.
We start our exploration of whole genome databases by taking a peek at the Viral Genome section available on the NCBI server. Working with complete viral genomes Viruses are fascinating objects, on the edge of the living world.
They function as minimal molecular bits of machinery, cleverly designed to ensure the mul- tiplication of nucleic-acid molecules the viral genome at the expense of cel- lular hosts eukaryotic, bacterial, or archaebacterial. While going about their business, viruses might go unnoticed — or trigger dreadful diseases and epidemics, such as smallpox, poliomyelitis, or AIDS.
On the black menu bar at the top of the form, click Genome. This takes you to the Entrez Genome page. Click the Viruses link on the right side of the form. The Viral Genomes reference page appears. Scroll down the Viral Reference Genomes page until you reach the table of available viral-genome sequences grouped by class Deltavirus, Retroid viruses, and so on , as shown in Figure Your browser returns a nice global summary of the HIV-1 genome, as shown in Figure At the bottom, a clickable picture indicates the identity and respective positions of all the genes.
Enter the name of your virus of interest. Click here for all proteins. Figure General structure of the HIV-1 genome. Click here for a live map. Click here to get gene details. Chapter 3: Using Nucleotide Sequence Databases 91 Similar pages are available for all viruses, regardless of their sizes.
Clicking the here link bottom of Figure gets you a live map, allowing you to zoom in on any genome region, down to the nucleotide sequence level, as shown in Figure Figure shows a position in the genome where the end of the Pol gene slightly overlaps with the beginning of the Vif gene. Viruses com- monly have the same nucleotide sequence involved in the making of two different amino-acid sequences. This takes you back to the HIV-1 Genome entry page.
Click the number 9 following Protein coding second column and row of the table. The Protein List page appears, as shown in Figure Figure Download- ing HIV-1 gene and protein sequences.
Working with complete bacterial genomes NCBI Entrez offers a nice interface to all publicly available complete bacterial genome sequences. For a quick tour, do the following: 1. Click Genome on the black menu bar near the top of the form. In the left dark-blue margin, click the Chromosome link located under the Bacteria heading. This step returns a listing of all bacteria whose chromosomes have been fully sequenced.
Directly clicking Bacteria would have given you a longer list, including parasitic DNA segment called plasmids. Figure shows the top of the list.
Figure The list of all available bacterial genome sequences top part. Your browser displays a table that summarizes the content and features of the bacterial genome.
Clicking the Here link near the bottom gets you the same type of live map we saw with the HIV-1 virus see the previous section , although the genome is now much larger. On this map, you can click to zoom into a particular region of the genome. The genome summary table contains numerous links to analyses pre-computed for all the genes function, similarity, evolutionary relationships that we leave you to try out for yourself.
Back in the Summary table refer to Figure click the Genome Project link. Doing so gets you a quick description of the bacterium, along with a pic- ture, details about its habitat, the disease it causes, and so on — as well as the reasons why it was important to decipher its genome sequence in the first place. Figure Bacillus anthracis strain Ames ancestor genome summary.
Figure Genome Project page for Bacillus anthracis strain Ames ancestor. Since then, they have con- tributed to more than 70 complete bacterial genomes, with more on the way. TIGR offers a site that is quite complementary to the NCBI resource because it keeps track of all ongoing bacterial genome sequencing projects not only of the completed ones , propose its own variety of well-integrated analysis tools for use, and offers the possibility to run similarity searches on its genome sequence data well before the actual completion of the projects themselves.
To pay them a quick visit, do the following: 1. A long list of micro-organisms appears, from which you get to select the one you are interested in. Select one microbe in the list, and then explore the various analyses tools by clicking the Genome Searches, Genome Toolbox, and Genome Analyses links at the top of each microbe-specific page.
Click here. Department of Energy DoE is also a main player in microbial genomics. Its Joint Genome Institute specializes in the study of organisms that are either a important for preserving or de-polluting our environ- ment, or b offering some new perspective in solving the incoming world- wide energy crisis such as cheap ways of producing hydrogen. To take a look at its data, follow these steps: 1. Point your browser to img. The Integrated Microbial Genomes resources home page appears, as shown in Figure A table of the available organisms appears.
Click here to start. Select an available organism by checking the corresponding box, then clicking Save Selections. The first organism, Aeropyrum pernix, would be a good choice for now.
Chapter 3: Using Nucleotide Sequence Databases 97 4. In the new page that appears, confirm your selection by clicking Compare Genomes. A Genome Statistics page appears. In the new page that appears, select a coordinate range for instance 1. This results in a live display of the microbe gene content in that range, as shown in Figure Putting the mouse pointer over the gene symbol gets you its name — and clicking the symbol provides you with a wealth of information on the corresponding protein.
Click on a gene symbol to find out more about its function. Exploring the Human Genome The sequencing of the human genome is probably one of the greatest scien- tific accomplishments of modern times. With million and then some nucleotides spread over 23 chromosomes, this genome is definitely a com- plex object to deal with. The major task ahead for bioinformatics is to inte- grate all the past, present, and future information that human genes contain in a maintainable, user-friendly resource.
This state of flux is true for all large animal genomes. Ideally, someone has to gather it all, package it nicely, and offer it to the whole research community for free! Having doubts that the last goal will ever be attainable in this less-than-perfect world?
Finding out about the Ensembl project The Internet home page of Ensembl www. This project — like the others we describe in this chapter — relies heavily on the collaboration of a large number of individual laboratories. It all started as part of the International Human Genome Project, continued for the Mouse Genome project, and is now being pursued for other animals. Data and software are also freely flow- ing among numerous national database and bioinformatics centers from all over the world, allowing a complex cross-linking to take place.
Getting started on the Ensembl site Considering how complex the human genome is, you may not be surprised to find that you can attack the Ensembl resources from many different angles. To quickly find out about your options, the best thing to do is to jump on the guided tour that Ensembl proposes on its home page. The impressive Ensembl home page appears, as shown in Figure Chapter 3: Using Nucleotide Sequence Databases 99 The page densely filled up with links, much too numerous to be explored in detail in this chapter.
You can literally spend weeks navigating all the possibilities. Thanks to them, you already learned the Latin species name for chim- panzee Pan troglodytes! Use BioMart for serious data mining. Click here to start navigating the human genome. Figure The Ensembl project home page.
Click the Homo sapiens icon. The page that appears see Figure presents a schematic image of the various human chromosomes numbered according to their size , including the sex chromosomes X and Y, as well as the DNA molecule of the human mitochondria a small energy-producing organelle present in all human cells.
Figure Starting your journey in the human genome. Click anywhere on the chromosome 15 picture. This lands you in the Chromosome 15 data subset Figure , within which we can now ask specific questions, such as: Where is the dUTPase gene?