Sequence Analysis in a Nutshell

by Markel, Scott; Leon, Darryl

• ISBN13: 9780596004941
• ISBN10: 059600494X
• Format: Paperback
• Copyright: 2003-01-01
• Publisher: Oreilly & Associates Inc

Summary

Sequence Analysis in a Nutshell accomplishes what no other book or bioinformatics information source has to this point: it pulls together vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis. The book is partitioned into three fundamental areas to help readers maximize their use of the content. Section 1, "Databases", contains examples of flatfiles from key databases (GenBank, EMBL, SWISS-PROT), the definitions of the codes or fields used in each database, and the sequence feature types/terms and qualifiers for the nucleotide and protein databases. Section 2, "Tools", provides the command line syntax for popular applications such as ReadSeq, MEME/MAST, BLAST, ClustalW, and the EMBOSS suite of analytical tools. Section 3, "Appendixes", concentrates on information essential to understanding the individual components that make up a biological sequence. The tables in this section include nucleotide and protein codes, genetic codes, as well as other relevant information.

Author Biography

Scott Markel is a Principal Software Architect at LION bioscience Inc., where he is responsible for providing architectural direction in the development of software for the life sciences, including the use and development of standards. He is a co-chair of the Life Sciences Research Domain Task Force of the Object Management Group, and also chairs the LSR's Architecture and Roadmap Working Group. Prior to working at LION, Scott worked at NetGenics, Johnson & Johnson Pharmaceutical Research & Development, and Sarnoff Corporation. He has a Ph.D. in mathematics from the University of Wisconsin-Madison. When Scott's not working or writing he enjoys spending time with his wife and kids, reading European history books, and just enjoying life in sunny San Diego.

Darryl León is a Principal Scientific Architect at LION bioscience Inc., where he is responsible for providing scientific direction in the development of software for the life sciences. Prior to working at LION, Darryl worked at NetGenics, DoubleTwist, and Genset. He has taught at California Polytechnic State University, San Luis Obispo, and currently teaches a bioinformatics class at U.C. Santa Cruz Extension and U.C. San Diego Extension. He is also a member of the Bioinformatics Advisory Committee at U.C. San Diego Extension. Darryl has a Ph. D. in biochemistry from the University of California, San Diego and did his postdoctoral research at the University of California, Santa Cruz.

Table of Contents

Preface	p. ix
Data Formats
FASTA Format	p. 3
NCBI's Sequence Identifier Syntax	p. 4
NCBI's Non-Redundant Database Syntax	p. 5
References	p. 5
GenBank/EMBL/DDBJ	p. 6
Example Flat Files	p. 6
GenBank Example Flat File	p. 6
DDBJ Example Flat File	p. 8
GenBank/DDBJ Field Definitions	p. 9
EMBL Example Flat File	p. 11
EMBL Field Definitions	p. 12
DDBJ/EMBL/GenBank Feature Table	p. 13
References	p. 22
SWISS-PROT	p. 23
SWISS-PROT Example Flat File	p. 23
SWISS-PROT Field Definitions	p. 28
SWISS-PROT Feature Table	p. 28
References	p. 32
Pfam	p. 33
Pfam Example Flat File	p. 33
Pfam Field Definitions	p. 35
References	p. 36
PROSITE	p. 37
PROSITE Example Flat File	p. 37
PROSITE Field Definitions	p. 39
References	p. 40
Tools
Readseq	p. 43
Supported Formats	p. 43
Command-Line Options	p. 44
References	p. 46
BLAST	p. 47
formatdb	p. 47
blastall	p. 48
megablast	p. 50
blastpgp	p. 51
PSI-BLAST	p. 52
PHI-BLAST	p. 53
b12seq	p. 53
References	p. 54
BLAT	p. 55
Command-Line Options	p. 56
References	p. 57
ClustalW	p. 58
Command-Line Options	p. 58
References	p. 61
HMMER	p. 62
hmmalign	p. 62
hmmbuild	p. 62
hmmcalibrate	p. 63
hmmconvert	p. 63
hmmemit	p. 63
hmmfetch	p. 64
hmmindex	p. 64
hmmpfam	p. 64
hmmsearch	p. 64
References	p. 65
MEME/MAST	p. 66
MEME	p. 66
MAST	p. 69
References	p. 72
EMBOSS	p. 73
Common Themes	p. 73
List of All EMBOSS Programs	p. 86
Details of EMBOSS Programs	p. 90
References	p. 241
Appendixes
Nucleotide and Amino Acid Tables	p. 245
Genetic Codes	p. 252
Resources	p. 265
Future Plans	p. 272
Index	p. 275
Table of Contents provided by Syndetics. All Rights Reserved.