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Sequence Analysis A Guide to Tools and Databases

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ISBN-10: 059600494X

ISBN-13: 9780596004941

Edition: 2003

Authors: Scott Markel, Darryl Le�n

List price: $29.95
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Gene sequence data is the most abundant type of data available, and if you're interested in analyzing it, you'll find a wealth of computational methods and tools to help you. In fact, finding the data is not the challenge at all; rather it is dealing with the plethora of flat file formats used to process the sequence entries and trying to remember what their specific field codes mean. If you survive by surrounding yourself with well-thumbed hard copies of readme files or remembering exactly where to look for the details when you need them, then "Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases is for you. This book is a handy resource, as well as an invaluable…    
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Book details

List price: $29.95
Copyright year: 2003
Publisher: O'Reilly Media, Incorporated
Publication date: 2/6/2003
Binding: Paperback
Pages: 304
Size: 6.00" wide x 9.00" long x 0.75" tall
Weight: 0.946
Language: English

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…    

Preface
Data Formats
FASTA Format
NCBI's Sequence Identifier Syntax
NCBI's Non-Redundant Database Syntax
References
GenBank/EMBL/DDBJ
Example Flat Files
GenBank Example Flat File
DDBJ Example Flat File
GenBank/DDBJ Field Definitions
EMBL Example Flat File
EMBL Field Definitions
DDBJ/EMBL/GenBank Feature Table
References
SWISS-PROT
SWISS-PROT Example Flat File
SWISS-PROT Field Definitions
SWISS-PROT Feature Table
References
Pfam
Pfam Example Flat File
Pfam Field Definitions
References
PROSITE
PROSITE Example Flat File
PROSITE Field Definitions
References
Tools
Readseq
Supported Formats
Command-Line Options
References
BLAST
formatdb
blastall
megablast
blastpgp
PSI-BLAST
PHI-BLAST
b12seq
References
BLAT
Command-Line Options
References
ClustalW
Command-Line Options
References
HMMER
hmmalign
hmmbuild
hmmcalibrate
hmmconvert
hmmemit
hmmfetch
hmmindex
hmmpfam
hmmsearch
References
MEME/MAST
MEME
MAST
References
EMBOSS
Common Themes
List of All EMBOSS Programs
Details of EMBOSS Programs
References
Appendixes
Nucleotide and Amino Acid Tables
Genetic Codes
Resources
Future Plans
Index