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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
ERP and Data Warehousing in Organizations: Issues and Challenges
Challenging the Unpredictable: Changeable Order Management Systems
ERP System Acquisition: A Process Model and Results From an Austrian Survey
The Second Wave ERP Market: An Australian Viewpoint
Data Mining for Business Process Reengineering
Development of Interactive Web Sites to Enhance Police/Community Relations
Cisco IP Communications Express: CallManager Express with Cisco Unity Express
Cisco IPC Express System Components
Cisco IPC Express System Architecture
Summary
Using Private Lines
Troubleshooting Phone Registration
Junos Cookbook (Cookbooks (OReilly))
Including Comments in the Configuration
Turning On Logging
Authenticating NTP
Rate-Limiting Traffic Flow to the Routing Engine
Prioritizing LSPs
HTI+ Home Technology Integrator & CEDIA Installer I All-In-One Exam Guide
Codes, Standards, and Safety Practices
Distributed Audio System Basics
Troubleshooting Video Systems
Installing a Home Lighting Control System
Appendix C Home Technology Industry Associations and Organizations
Extending and Embedding PHP
Data Retrieval
Arg Info and Type-hinting
Summary
Accessing Streams
Summary
.NET-A Complete Development Cycle
Unit Tests
References for Further Reading
Conclusion
References for Further Reading
Requirements Tracing
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