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 |