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Genomics and Bioinformatics: An Introduction to Programming Tools for Life Scientists [Pehme köide]

4.33/5 (12 hinnangut Goodreads-ist)
(Göteborgs Universitet, Sweden)
  • Formaat: Paperback / softback, 358 pages, kõrgus x laius x paksus: 245x189x17 mm, kaal: 770 g, Worked examples or Exercises; 23 Tables, black and white; 20 Halftones, unspecified; 70 Halftones, color
  • Ilmumisaeg: 07-Jun-2012
  • Kirjastus: Cambridge University Press
  • ISBN-10: 1107401240
  • ISBN-13: 9781107401242
Teised raamatud teemal:
Genomics and Bioinformatics: An Introduction to Programming Tools for Life ScientistsSuurem pilt
  • Formaat: Paperback / softback, 358 pages, kõrgus x laius x paksus: 245x189x17 mm, kaal: 770 g, Worked examples or Exercises; 23 Tables, black and white; 20 Halftones, unspecified; 70 Halftones, color
  • Ilmumisaeg: 07-Jun-2012
  • Kirjastus: Cambridge University Press
  • ISBN-10: 1107401240
  • ISBN-13: 9781107401242
Teised raamatud teemal:
Püsilink: https://www.kriso.ee/db/9781107401242.html
Märksõnad:
"With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems"--

A hands-on introduction to Unix, Perl and other bioinformatics tools using relevant and interesting molecular biology problems.

Arvustused

'The book provides a lively and accessible introduction to current research in the life sciences, and it does so in a succinct way by grounding the explanations with simple algorithms expressed in Perl code. As such, the book can be very useful to a general science audience, particularly those with a computer science background, whether established researchers or undergraduate students. The writing is inspiring and engaging, and the inclusion of Perl code makes it easy for readers to apply the knowledge and observe the outcomes.' Sara Kalvala, Computing Reviews

Muu info

A hands-on introduction to Unix, Perl and other bioinformatics tools using relevant and interesting molecular biology problems.
Preface xi
Acknowledgements xiv
Design and conventions of this book xvi
1 Introduction: working with the molecules of life in the computer
1(18)
Life on Earth and evolution
2(2)
The machinery of genetic information: more about DNA
4(3)
Genes and genomes
7(1)
Genes at work: transcription and translation
8(3)
Organization of the human genome
11(1)
Inferring products of DNA replication
12(2)
Inferring RNA products of transcription
14(1)
Inferring protein products of translation
14(3)
Exercises
17(2)
2 Gene technology: cutting DNA
19(12)
Early days of restriction enzymes
20(1)
Properties of restriction enzymes
21(2)
Pattern matching
23(1)
Identifying restriction enzyme sites with Perl
24(5)
Exercises
29(2)
3 Gene technology: knocking genes down
31(13)
Interfering with gene expression
31(1)
Small silencing RNAs
32(2)
RNAi: functions and applications
34(1)
Silencing RNAs and design principles
35(2)
Identifying siRNA candidates
37(5)
Exercises
42(2)
4 Gene technology: amplifying DNA
44(11)
What is PCR?
44(2)
PCR applications
46(1)
Primer design
46(2)
Reverse translation
48(3)
Good manners during Perl programming
51(3)
Exercises
54(1)
5 Human disease: when DNA sequences are toxic
55(11)
Inherited disease and changes in DNA
55(2)
Huntington's disease and CAG repeat expansion
57(2)
Identifying mRNAs with CAG repeats
59(6)
Exercises
65(1)
6 Human disease: iron imbalance and the iron responsive element
66(8)
An inherited disease affecting the iron-binding protein ferritin
66(1)
Many proteins of iron metabolism are regulated at the level of translation
66(2)
Structure of the iron responsive element
68(1)
Identifying the iron responsive element
69(3)
Exercises
72(2)
7 Human disease: cancer as a result of aberrant proteins
74(18)
Cancer as a genetic disease
74(1)
Cancer and DNA repair
75(1)
Chromosome rearrangements and the Philadelphia chromosome
76(1)
Dotplots and alignments
77(4)
BLAST
81(2)
Using BLAST to examine the BCR-ABL fusion protein
83(7)
Exercises
90(2)
8 Evolution: what makes us human?
92(13)
Genetic differences between humans and chimpanzees
92(1)
A protein related to human speech
93(1)
FOXP2 in other animals
94(1)
Comparing FOXP2 in different animals
95(6)
Changes in FOXP2 specific to humans
101(1)
Exercises
102(3)
9 Evolution: resolving a criminal case
105(16)
A fatal injection
105(1)
Methods of molecular phylogeny
106(7)
Examination of the criminal case
113(7)
Exercises
120(1)
10 Evolution: the sad case of the Tasmanian tiger
121(16)
Extinction
121(1)
The thylacine
122(1)
Tiger history
123(2)
Recent DNA analysis
125(1)
Inferring the phylogeny of marsupials
126(3)
Examining taxonomy
129(6)
Exercises
135(2)
11 A function to every gene: termites, metagenomics and learning about the function of a sequence
137(13)
Assigning function based on sequence similarity
137(1)
Metagenomics
138(1)
The other genome
139(1)
Termites and cellulose digestion
140(1)
Assigning function to termite sequences
141(6)
Exercises
147(3)
12 A function to every gene: royal blood and order in the sequence universe
150(14)
Royal disease
150(1)
Blood-clotting pathways
151(2)
Protein domain architecture
153(1)
Bioinformatics of protein domains
154(2)
Bioinformatic analysis of blood-clotting proteins
156(4)
Evolution of blood clotting
160(2)
Exercises
162(2)
13 A function to every gene: a slimy molecule
164(9)
Extensive sugar decoration
164(1)
Mucins and repeats
165(3)
Computational identification of mucin domains
168(3)
Exercises
171(2)
14 Information resources: learning about flu viruses
173(25)
Short history of sequence databases
173(2)
Features of nucleotide sequence databases
175(2)
Comparative genomics
177(1)
Protein sequence and structure data
178(2)
Exploring databases at the NCBI
180(1)
NCBI databases in eUtils
181(1)
NCBI query syntax
182(3)
The Entrez Programming Utilities
185(1)
Parameters supplied to eUtils: scripts and construction of URLs
185(2)
EFetch
187(1)
ESearch
188(4)
Further analysis of influenza viruses: extracting and filtering information with Perl and Unix tools
192(3)
ELink
195(1)
Exercises
196(1)
NCBI documentation resources
196(2)
15 Finding genes: going ashore at CpG islands
198(10)
Transcription and its regulation
198(1)
DNA sequences that influence transcription
199(1)
CpG islands
200(2)
Finding CpG islands
202(4)
Exercises
206(2)
16 Finding genes: in the world of snurps
208(14)
Methods of gene prediction
208(1)
The splicing machinery
209(4)
Constructing a PSSM
213(3)
Scoring with a PSSM
216(3)
Exercises
219(3)
17 Finding genes: hunting for the distant RNA relatives
222(19)
The RNA world
222(1)
Properties of RNA and computational RNA finding
223(4)
An RNA involved in protein transport
227(1)
The organelles and their evolution
227(2)
The quest for chloroplast RNAs
229(8)
Automating tasks with Unix and Perl
237(1)
Exercises
238(3)
18 Personal genomes: the differences between you and me
241(11)
Personal genomes
241(1)
Individual variation and SNPs
242(2)
Counting SNPs
244(6)
Exercises
250(2)
19 Personal genomes: what's in my genome?
252(14)
Human roots
252(1)
An SNP dataset of South African individuals
253(3)
What SNPs are unique to the Bushmen?
256(1)
What SNPs are in coding regions?
257(3)
A bitter taste
260(3)
Constructing your own modules
263(1)
Exercises
264(2)
20 Personal genomes: details of family genetics
266(12)
Basic principles of genetic inheritance
266(3)
Analysis of a family quartet
269(3)
Where are the crossing-over sites?
272(5)
Exercises
277(1)
Appendix I brief Unix reference 278(11)
Appendix II a selection of biological sequence analysis software 289(11)
Appendix III a short Perl reference 300(23)
Appendix IV a brief introduction to R 323(7)
Index 330
Tore Samuelsson is a Professor in Biochemistry and Bioinformatics at the Institute of Biomedicine, University of Gothenburg, Sweden. He has been active in bioinformatics research for more than fifteen years and has over ten years' experience of teaching in the field, including the development of web resources for molecular biology and bioinformatics education.