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


Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis. The book contains details and examples of the common database formats (GenBank, EMBL, SWISS-PROT) and the GenBank/EMBL/DDBJ Feature Table Definitions. It also provides the command line syntax for popular analysis applications such as Readseq and MEME/MAST, BLAST, ClustalW, and the EMBOSS suite, as well as tables of nucleotide, genetic, and amino acid codes. Written in O'Reilly's enormously popular, straightforward "Nutshell" format, this book draws together essential information for bioinformaticians in industry and academia, as well as for students. If sequence analysis is part of your daily life, you'll want this easy-to-use book on your desk.

   
•  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