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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
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Multiple Documents
Enabling Drag and Drop
Creating Data-Aware Forms
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Multithreading
Managing Enterprise Systems with the Windows Script Host
Logon Scripts and Scheduling
Registry Operations
Application Automation
Network Administration/WMI
Security
Service-Oriented Architecture (SOA): Concepts, Technology, and Design
Notification and eventing
Considerations for positioning core SOA standards
WS-BPEL language basics
Integration considerations
Appendix B. Service Models Reference
Microsoft VBScript Professional Projects
Archive Management
Reporting Application Summary Data via the Web
Designing the Web Site
Converting Reports to HTML Pages
Appendix B Whats on the Companion Web Site
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Basic Commands to Get Started
Setting Up a Drawing
Gaining Drawing Strategies: Part 1
Generating Elevations
Dimensioning a Drawing
GDI+ Programming with C#
Understanding GDI+
Understanding and Using Brushes
Text Transformation
Drawing a Pie Chart
Understanding the SetStyle Method
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