Books & Videos

Table of Contents

  1. 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
  2. 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
  3. Appendixes

    1. Appendix Nucleotide andAmino Acid Tables

      1. Nucleotide Codes
      2. Amino Acid Codes
      3. References
    2. Appendix 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 Resources

      1. Web Sites
      2. Books
      3. Journal Articles
    4. Appendix Future Plans

  1. Colophon