Perl Programming for Biologists

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John Wiley & Sons, Jul 14, 2003 - Medical - 208 pages
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Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusable and maintainable scripts that spare the rote repetition of code.
 

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Contents

Introduction
3
Control Structures
4
Variables and Data Types
13
Arrays and Hashes
27
Perl Programming for Biologists D Curtis Jamison
43
1
52
Subroutines
63
77699
69
Programming Challenges
162
Appendix A Partial Perl Reference
163
Chapter 5
164
Chapter 8
165
Appendix B Bioinformatics File Formats
167
ASN 1
170
EMBL
175
17
176

String Manipulation
75
Input and Output
89
Perl Modules and Packages
105
11
120
References
125
ObjectOriented Programming
133
Bioperl
147
For More Information
161
PDB
177
Fasta
181
BLAST
182
ACEDB
183
Index
185
44
186
89
188
Copyright

Other editions - View all

Perl Programming For Bioinformatics & Biologists
D. Curtis Jamison
No preview available - 2003

Common terms and phrases

accessors actually argument array assign associated ATOM attributes base beginning Bioperl bless called CFTR Chapter character code block command common complex condition CONECT constructor contains count CPAN create data structure database default defined entries example execute expression Fasta Figure filehandle Finally format function GenBank gene going hash input install iterate language length letter look loop match method module Note object object-oriented operator output package passed pattern Perl Perl Programming places position primer pair provides RandomSeq record reference regular REMARK REMARK replace retval reverse scalar script sequence shift simply single sort specific statement stored strict string subroutine switch takes things true Unix variable write

About the author (2003)

Curtis Jamison received his B.A. (Molecular, Cellular and Developmental Biology) from the University of Colorado, Boulder in 1985, and his Ph.D. (Biological Sciences) from the University of Denver in 1991. He held an NSF CISE postdoctoral fellowship while at National Center for Supercomputing Applications, University of Illinois, Champaign-Urbana, where he received a patent for his work on distributed application gateways and database federation. Dr. Jamison continued his work on database federation with plant genome databases for the USDA Agricultural Genome Information Service, and then later evolved to work on higher organisms at the National Institutes of Health where he created computational tools for genome mapping for the Human Genome Project. He is currently an Associate Professor of Bioinformatics at George Mason University, and is director of the Bioinformatics Ph.D. program.

Bibliographic information

QR code for Perl Programming for Biologists
TitlePerl Programming for Biologists
AuthorD. Curtis Jamison
Editionillustrated
PublisherJohn Wiley & Sons, 2003
ISBN0471430595, 9780471430599
Length208 pages
Subjects ›  › 

Medical / Immunology
Science / Life Sciences / General
  
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