Sequence Analysis in a Nutshell: A Guide to Tools

Description

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.

Full Description

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 reference, for anyone who needs to know about the practical aspects and mechanics of sequence analysis. 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 is partitioned into three fundamental areas to help you maximize your use of the content. The first section, "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. The second section, "Tools" provides the command line syntax for popular applications such as ReadSeq, MEME/MAST, BLAST, ClustalW, and the EMBOSS suite of analytical tools. The third section, "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. 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

Data Formats
1. Chapter 1 FASTA Format
  1. NCBI's Sequence Identifier Syntax
  2. NCBI's Non-Redundant Database Syntax
  3. References
2. Chapter 2 GenBank/EMBL/DDBJ
  1. Example Flat Files
  2. GenBank Example Flat File
  3. DDBJ Example Flat File
  4. GenBank/DDBJ Field Definitions
  5. EMBL Example Flat File
  6. EMBL Field Definitions
  7. DDBJ/EMBL/GenBank Feature Table
  8. References
3. Chapter 3 SWISS-PROT
  1. SWISS-PROT Example Flat File
  2. SWISS-PROT Field Definitions
  3. SWISS-PROT Feature Table
  4. References
4. Chapter 4 Pfam
  1. Pfam Example Flat File
  2. Pfam Field Definitions
  3. References
5. Chapter 5 PROSITE
  1. PROSITE Example Flat File
  2. PROSITE Field Definitions
  3. References
Tools
1. Chapter 6 Readseq
  1. Supported Formats
  2. Command-Line Options
  3. References
2. Chapter 7 BLAST
  1. formatdb
  2. blastall
  3. megablast
  4. blastpgp
  5. PSI-BLAST
  6. PHI-BLAST
  7. bl2seq
  8. References
3. Chapter 8 BLAT
  1. Command-Line Options
  2. References
4. Chapter 9 ClustalW
  1. Command-Line Options
  2. References
5. Chapter 10 HMMER
  1. hmmalign
  2. hmmbuild
  3. hmmcalibrate
  4. hmmconvert
  5. hmmemit
  6. hmmfetch
  7. hmmindex
  8. hmmpfam
  9. hmmsearch
  10. References
6. Chapter 11 MEME/MAST
  1. MEME
  2. MAST
  3. References
7. Chapter 12 EMBOSS
  1. Common Themes
  2. List of All EMBOSS Programs
  3. Details of EMBOSS Programs
  4. aaindexextract
  5. abiview
  6. alignwrap
  7. antigenic
  8. backtranseq
  9. banana
  10. biosed
  11. btwisted
  12. cai
  13. chaos
  14. charge
  15. checktrans
  16. chips
  17. cirdna
  18. codcmp
  19. coderet
  20. compseq
  21. cons
  22. contacts
  23. cpgplot
  24. cpgreport
  25. cusp
  26. cutgextract
  27. cutseq
  28. dan
  29. dbiblast
  30. dbifasta
  31. dbiflat
  32. dbigcg
  33. degapseq
  34. descseq
  35. dichet
  36. diffseq
  37. digest
  38. distmat
  39. domainer
  40. dotmatcher
  41. dotpath
  42. dottup
  43. dreg
  44. einverted
  45. embossdata
  46. embossversion
  47. emma
  48. emowse
  49. entret
  50. eprimer3
  51. equicktandem
  52. est2genome
  53. etandem
  54. extractfeat
  55. extractseq
  56. findkm
  57. freak
  58. funky
  59. fuzznuc
  60. fuzzpro
  61. fuzztran
  62. garnier
  63. geecee
  64. getorf
  65. helixturnhelix
  66. hetparse
  67. hmmgen
  68. hmoment
  69. iep
  70. infoalign
  71. infoseq
  72. interface
  73. isochore
  74. lindna
  75. listor
  76. marscan
  77. maskfeat
  78. maskseq
  79. matcher
  80. megamerger
  81. merger
  82. msbar
  83. mwcontam
  84. mwfilter
  85. needle
  86. newcpgreport
  87. newcpgseek
  88. newseq
  89. noreturn
  90. notseq
  91. nrscope
  92. nthseq
  93. octanol
  94. oddcomp
  95. palindrome
  96. pasteseq
  97. patmatdb
  98. patmatmotifs
  99. pdbparse
  100. pdbtosp
  101. pepcoil
  102. pepinfo
  103. pepnet
  104. pepstats
  105. pepwheel
  106. pepwindow
  107. pepwindowall
  108. plotcon
  109. plotorf
  110. polydot
  111. preg
  112. prettyplot
  113. prettyseq
  114. primersearch
  115. printsextract
  116. profgen
  117. profit
  118. prophecy
  119. prophet
  120. prosextract
  121. pscan
  122. psiblast
  123. rebaseextract
  124. recoder
  125. redata
  126. remap
  127. restover
  128. restrict
  129. revseq
  130. scopalign
  131. scope
  132. scopnr
  133. scopparse
  134. scoprep
  135. scopreso
  136. scopseqs
  137. seealso
  138. seqalign
  139. seqmatchall
  140. seqnr
  141. seqret
  142. seqretsplit
  143. seqsearch
  144. seqsort
  145. seqwords
  146. showalign
  147. showdb
  148. showfeat
  149. showorf
  150. showseq
  151. shuffleseq
  152. sigcleave
  153. siggen
  154. sigscan
  155. silent
  156. skipseq
  157. splitter
  158. stretcher
  159. stssearch
  160. supermatcher
  161. swissparse
  162. syco
  163. textsearch
  164. tfextract
  165. tfm
  166. tfscan
  167. tmap
  168. tranalign
  169. transeq
  170. trimest
  171. trimseq
  172. union
  173. vectorstrip
  174. water
  175. whichdb
  176. wobble
  177. wordcount
  178. wordmatch
  179. wossname
  180. yank
  181. References
Appendixes
1. Appendix A Nucleotide andAmino Acid Tables
  1. Nucleotide Codes
  2. Amino Acid Codes
  3. References
2. Appendix B Genetic Codes
  1. The Standard Code
  2. Vertebrate Mitochondrial Code
  3. Yeast Mitochondrial Code
  4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
  5. Invertebrate Mitochondrial Code
  6. Ciliate, Dasycladacean, and Hexamita Nuclear Code
  7. Echinoderm and Flatworm Mitochondrial Code
  8. Euplotid Nuclear Code
  9. Bacterial and Plant Plastid Code
  10. Alternative Yeast Nuclear Code
  11. Ascidian Mitochondrial Code
  12. Alternative Flatworm Mitochondrial Code
  13. Blepharisma Nuclear Code
  14. Chlorophycean Mitochondrial Code
  15. Trematode Mitochondrial Code
  16. Scenedesmus Obliquus Mitochondrial Code
  17. Thraustochytrium Mitochondrial Code
  18. References
3. Appendix C Resources
  1. Web Sites
  2. Books
  3. Journal Articles
4. Appendix D Future Plans

Colophon

Product Details

Title:

Sequence Analysis in a Nutshell: A Guide to Tools

By:

Scott Markel, Darryl Leon

Publisher:

O'Reilly Media

Formats:

Print
Safari Books Online

Print Release:

January 2003

Pages:

304

Print ISBN:

978-0-596-00494-1

| ISBN 10:

0-596-00494-X

Customer Reviews

About the Authors

Scott Markel

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.

View Scott Markel's full profile page.
Darryl Leon

Darryl LeÃ³n 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.

View Darryl Leon's full profile page.

Colophon

Our look is the result of reader comments, our own experimentation, and feedback from distribution channels. Distinctive covers complement our distinctive approach to technical topics, breathing personality and life into potentially dry subjects. The animal on the cover of Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases is a liger. Much like sequence analysis, which is a cross between computer science and biology, a liger is the result of a cross between a lion and a tigress. Tigons, which are the offspring of a tiger and a lioness, have also been bred.

In a classic display of "hybrid vigor," a liger may be 10-12 feet in length and weigh upwards of 800-1,000 pounds, making it significantly larger than either of its parents. Since lions and tigers are genetically very similar, their offspring show a fascinating blend of the features and habits of both species. Depending on which subspecies of lion and tiger are bred together, and how their genes combine, a liger may look more tigerish or more lionish. Ligers are both striped and spotted; the spots being inherited from the lion. A male liger may grow a leonine mane or the facial ruff of a tiger. Female ligers exhibit both the leonine need for social interaction and the tiger-like need for solitude. Both sexes roar like lions and "chuff" like tigers, and most ligers also inherit their tiger parent's love of water. Like other interspecies hybrids, ligers are usually sterile.

Ligers do not occur in the wild, but are the result of captive breeding. Natural breeding is not impossible, just extremely unlikely since the habitats of tigers and lions have little to no overlap, and because the solitary tiger would most likely avoid interacting with a pride of lions. Philip Dangler was the production editor and copyeditor for Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases. Emily Quill, Linley Dolby, and Claire Cloutier provided quality control. Judy Hoer provided production assistance. Nancy Crumpton wrote the index.

Ellie Volckhausen designed the cover of this book, based on a series design by Edie Freedman. The cover image is an original illustration created by Lorrie LeJeune. Emma Colby produced the cover layout with QuarkXPress 4.1 using Adobe's ITC Garamond font.

David Futato designed the interior layout. This book was converted by Joe Wizda and Mike Sierra to FrameMaker 5.5.6 with a format conversion tool created by Erik Ray, Jason McIntosh, Neil Walls, and Mike Sierra that uses Perl and XML technologies. The text font is Linotype Birka; the heading font is Adobe Myriad Condensed; and the code font is LucasFont's TheSans Mono Condensed. The illustrations that appear in the book were produced by Robert Romano and Jessamyn Read using Macromedia FreeHand 9 and Adobe Photoshop 6. This colophon was written by Lorrie LeJeune.

O'Reilly Books & Videos

Sequence Analysis in a Nutshell: A Guide to Tools

A Guide to Common Tools and Databases

Data Formats

Chapter 1 FASTA Format

Chapter 2 GenBank/EMBL/DDBJ

Chapter 3 SWISS-PROT

Chapter 4 Pfam

Chapter 5 PROSITE

Tools

Chapter 6 Readseq

Chapter 7 BLAST

Chapter 8 BLAT

Chapter 9 ClustalW

Chapter 10 HMMER

Chapter 11 MEME/MAST

Chapter 12 EMBOSS

Appendixes

Appendix A Nucleotide andAmino Acid Tables

Appendix B Genetic Codes

Appendix C Resources

Appendix D Future Plans

Colophon

Scott Markel

Darryl Leon