Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
EAN: 2147483647
Year: 2005
Pages: 312
Pages: 312
- Main Page
- Table of content
- 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
- 1.1 NCBI s Sequence Identifier Syntax
- 1.2 NCBI s Non-Redundant Database Syntax
- 1.3 References
- Chapter 2. GenBankEMBLDDBJ
- 2.1 Example Flat Files
- 2.2 GenBank Example Flat File
- 2.3 DDBJ Example Flat File
- 2.4 GenBankDDBJ Field Definitions
- 2.5 EMBL Example Flat File
- 2.6 EMBL Field Definitions
- 2.7 DDBJEMBLGenBank Feature Table
- 2.8 References
- Chapter 3. SWISS-PROT
- 3.1 SWISS-PROT Example Flat File
- 3.2 SWISS-PROT Field Definitions
- 3.3 SWISS-PROT Feature Table
- 3.4 References
- Chapter 4. Pfam
- 4.1 Pfam Example Flat File
- 4.2 Pfam Field Definitions
- 4.3 References
- Chapter 5. PROSITE
- 5.1 PROSITE Example Flat File
- 5.2 PROSITE Field Definitions
- 5.3 References
- Part II: Tools
- Chapter 6. Readseq
- 6.1 Supported Formats
- 6.2 Command-Line Options
- 6.3 References
- Chapter 7. BLAST
- formatdb
- blastall
- megablast
- blastpgp
- PSI-BLAST
- PHI-BLAST
- bl2seq
- 7.1 References
- Chapter 8. BLAT
- 8.1 Command-Line Options
- 8.2 References
- Chapter 9. ClustalW
- 9.1 Command-Line Options
- 9.2 References
- Chapter 10. HMMER
- hmmalign
- hmmbuild
- hmmcalibrate
- hmmconvert
- hmmemit
- hmmfetch
- hmmindex
- hmmpfam
- hmmsearch
- 10.1 References
- Chapter 11. MEMEMAST
- 11.1 MEME
- 11.2 MAST
- 11.3 References
- Chapter 12. EMBOSS
- 12.1 Common Themes
- 12.2 List of All EMBOSS Programs
- 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
- 12.4 References
- Part III: Appendixes
- Appendix A. Nucleotide andAmino Acid Tables
- A.1 Nucleotide Codes
- A.2 Amino Acid Codes
- A.3 References
- Appendix B. Genetic Codes
- B.1 The Standard Code
- B.2 Vertebrate Mitochondrial Code
- B.3 Yeast Mitochondrial Code
- B.4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the MycoplasmaSpiroplasma Code
- B.5 Invertebrate Mitochondrial Code
- B.6 Ciliate, Dasycladacean, and Hexamita Nuclear Code
- B.7 Echinoderm and Flatworm Mitochondrial Code
- B.8 Euplotid Nuclear Code
- B.9 Bacterial and Plant Plastid Code
- B.10 Alternative Yeast Nuclear Code
- B.11 Ascidian Mitochondrial Code
- B.12 Alternative Flatworm Mitochondrial Code
- B.13 Blepharisma Nuclear Code
- B.14 Chlorophycean Mitochondrial Code
- B.15 Trematode Mitochondrial Code
- B.16 Scenedesmus Obliquus Mitochondrial Code
- B.17 Thraustochytrium Mitochondrial Code
- B.18 References
- Appendix C. Resources
- C.1 Web Sites
- C.2 Books
- C.3 Journal Articles
- Appendix D. Future Plans
- crystalball
- Colophon
- Index
- Index SYMBOL
- Index A
- Index B
- Index C
- Index D
- Index E
- Index F
- Index G
- Index H
- Index I
- Index J
- Index K
- Index L
- Index M
- Index N
- Index O
- Index P
- Index Q
- Index R
- Index S
- Index T
- Index U
- Index V
- Index W
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
EAN: 2147483647
Year: 2005
Pages: 312
Pages: 312
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