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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
Year: 2005
Pages: 312
Authors:
Darryl Leon
,
Scott Markel
,
Lorrie LeJeune
BUY ON AMAZON
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
Year: 2005
Pages: 312
Authors:
Darryl Leon
,
Scott Markel
,
Lorrie LeJeune
BUY ON AMAZON
Project Management JumpStart
Developing Project Management Skills
Developing the Project Plan
Budgeting 101
Appendix A Answers to Review Questions
Appendix C Sample Project Management Checklists
WebLogic: The Definitive Guide
Using JavaMail
Building CMP Entity Beans
The Java Security Manager
The Security Provider Architecture
Timer MBeans
Microsoft VBScript Professional Projects
Conditional Logic and Iterative Structures
VBScript and the WSH
Project Case Study Analyzing Application Logs
Scheduling Script Execution
Converting Reports to HTML Pages
After Effects and Photoshop: Animation and Production Effects for DV and Film, Second Edition
Photoshop Layers and After Effects
Exaggeration Equals Characterization
Rotoscoping Techniques with Photoshop
Matte and Keying Plug-ins
Color, Light, and Focus
Lean Six Sigma for Service : How to Use Lean Speed and Six Sigma Quality to Improve Services and Transactions
The ROI of Lean Six Sigma for Services
Executing Corporate Strategy with Lean Six Sigma
Using DMAIC to Improve Service Processes
First Wave Service Projects
Designing World-Class Services (Design for Lean Six Sigma)
Extending and Embedding PHP
Summary
Functional Functions
Summary
Overriding INI_SYSTEM and INI_PERDIR Options
Memory
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