Sequence analysis in a nutshell : a guide to tools and databases

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 [ Team LiB ]