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•	Table of Contents
•	Index
•	Reviews
•	Reader Reviews
•	Errata

Sequence Analysis in a Nutshell
By Darryl Leon, Scott Markel
Publisher	: O'Reilly
Pub Date	: January 2003
ISBN	: 0-596-00494-X
Pages	: 302

		Copyright
		Preface
			Sequence Analysis Tools and Databases
			How This Book Is Organized
			Assumptions This Book Makes
			Conventions Used in This Book
			How to Contact Us
			Acknowledgments
		Part I:  Data Formats
			Chapter 1.  FASTA Format
				Section 1.1.  NCBI's Sequence Identifier Syntax
				Section 1.2.  NCBI's Non-Redundant Database Syntax
				Section 1.3.  References
			Chapter 2.  GenBank/EMBL/DDBJ
				Section 2.1.  Example Flat Files
				Section 2.2.  GenBank Example Flat File
				Section 2.3.  DDBJ Example Flat File
				Section 2.4.  GenBank/DDBJ Field Definitions
				Section 2.5.  EMBL Example Flat File
				Section 2.6.  EMBL Field Definitions
				Section 2.7.  DDBJ/EMBL/GenBank Feature Table
				Section 2.8.  References
			Chapter 3.  SWISS-PROT
				Section 3.1.  SWISS-PROT Example Flat File
				Section 3.2.  SWISS-PROT Field Definitions
				Section 3.3.  SWISS-PROT Feature Table
				Section 3.4.  References
			Chapter 4.  Pfam
				Section 4.1.  Pfam Example Flat File
				Section 4.2.  Pfam Field Definitions
				Section 4.3.  References
			Chapter 5.  PROSITE
				Section 5.1.  PROSITE Example Flat File
				Section 5.2.  PROSITE Field Definitions
				Section 5.3.  References
		Part II:  Tools
			Chapter 6.  Readseq
				Section 6.1.  Supported Formats
				Section 6.2.  Command-Line Options
				Section 6.3.  References
			Chapter 7.  BLAST
				formatdb
				blastall
				megablast
				blastpgp
				PSI-BLAST
				PHI-BLAST
				bl2seq
				Section 7.1.  References
			Chapter 8.  BLAT
				Section 8.1.  Command-Line Options
				Section 8.2.  References
			Chapter 9.  ClustalW
				Section 9.1.  Command-Line Options
				Section 9.2.  References
			Chapter 10.  HMMER
				hmmalign
				hmmbuild
				hmmcalibrate
				hmmconvert
				hmmemit
				hmmfetch
				hmmindex
				hmmpfam
				hmmsearch
				Section 10.1.  References
			Chapter 11.  MEME/MAST
				Section 11.1.  MEME
				Section 11.2.  MAST
				Section 11.3.  References
			Chapter 12.  EMBOSS
				Section 12.1.  Common Themes
				Section 12.2.  List of All EMBOSS Programs
				Section 12.3.  Details of EMBOSS Programs
				aaindexextract
				abiview
				alignwrap
				antigenic
				backtranseq
				banana
				biosed
				btwisted
				cai
				chaos
				charge
				checktrans
				chips
				cirdna
				codcmp
				coderet
				compseq
				cons
				contacts
				cpgplot
				cpgreport
				cusp
				cutgextract
				cutseq
				dan
				dbiblast
				dbifasta
				dbiflat
				dbigcg
				degapseq
				descseq
				dichet
				diffseq
				digest
				distmat
				domainer
				dotmatcher
				dotpath
				dottup
				dreg
				einverted
				embossdata
				embossversion
				emma
				emowse
				entret
				eprimer3
				equicktandem
				est2genome
				etandem
				extractfeat
				extractseq
				findkm
				freak
				funky
				fuzznuc
				fuzzpro
				fuzztran
				garnier
				geecee
				getorf
				helixturnhelix
				hetparse
				hmmgen
				hmoment
				iep
				infoalign
				infoseq
				interface
				isochore
				lindna
				listor
				marscan
				maskfeat
				maskseq
				matcher
				megamerger
				merger
				msbar
				mwcontam
				mwfilter
				needle
				newcpgreport
				newcpgseek
				newseq
				noreturn
				notseq
				nrscope
				nthseq
				octanol
				oddcomp
				palindrome
				pasteseq
				patmatdb
				patmatmotifs
				pdbparse
				pdbtosp
				pepcoil
				pepinfo
				pepnet
				pepstats
				pepwheel
				pepwindow
				pepwindowall
				plotcon
				plotorf
				polydot
				preg
				prettyplot
				prettyseq
				primersearch
				printsextract
				profgen
				profit
				prophecy
				prophet
				prosextract
				pscan
				psiblast
				rebaseextract
				recoder
				redata
				remap
				restover
				restrict
				revseq
				scopalign
				scope
				scopnr
				scopparse
				scoprep
				scopreso
				scopseqs
				seealso
				seqalign
				seqmatchall
				seqnr
				seqret
				seqretsplit
				seqsearch
				seqsort
				seqwords
				showalign
				showdb
				showfeat
				showorf
				showseq
				shuffleseq
				sigcleave
				siggen
				sigscan
				silent
				skipseq
				splitter
				stretcher
				stssearch
				supermatcher
				swissparse
				syco
				textsearch
				tfextract
				tfm
				tfscan
				tmap
				tranalign
				transeq
				trimest
				trimseq
				union
				vectorstrip
				water
				whichdb
				wobble
				wordcount
				wordmatch
				wossname
				yank
				Section 12.4.  References
		Part III:  Appendixes
			Appendix A.  Nucleotide andAmino Acid Tables
				Section A.1.  Nucleotide Codes
				Section A.2.  Amino Acid Codes
				Section A.3.  References
			Appendix B.  Genetic Codes
				Section B.1.  The Standard Code
				Section B.2.  Vertebrate Mitochondrial Code
				Section B.3.  Yeast Mitochondrial Code
				Section B.4.  Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
				Section B.5.  Invertebrate Mitochondrial Code
				Section B.6.  Ciliate, Dasycladacean, and Hexamita Nuclear Code
				Section B.7.  Echinoderm and Flatworm Mitochondrial Code
				Section B.8.  Euplotid Nuclear Code
				Section B.9.  Bacterial and Plant Plastid Code
				Section B.10.  Alternative Yeast Nuclear Code
				Section B.11.  Ascidian Mitochondrial Code
				Section B.12.  Alternative Flatworm Mitochondrial Code
				Section B.13.  Blepharisma Nuclear Code
				Section B.14.  Chlorophycean Mitochondrial Code
				Section B.15.  Trematode Mitochondrial Code
				Section B.16.  Scenedesmus Obliquus Mitochondrial Code
				Section B.17.  Thraustochytrium Mitochondrial Code
				Section B.18.  References
			Appendix C.  Resources
				Section C.1.  Web Sites
				Section C.2.  Books
				Section C.3.  Journal Articles
			Appendix D.  Future Plans
				crystalball
		Colophon
		Index

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