Blast: [an essential guide to the basic local alignment search tool]
Gespeichert in:
| Hauptverfasser: | , , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Beijing [u.a.]
O'Reilly
2003
|
| Ausgabe: | 1. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XVIII, 339 S. graph. Darst. |
| ISBN: | 0596002998 9780596002992 |
Internformat
MARC
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| 020 | |a 0596002998 |9 0-596-00299-8 | ||
| 020 | |a 9780596002992 |9 978-0-596-00299-2 | ||
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| 084 | |a BIO 110f |2 stub | ||
| 100 | 1 | |a Korf, Ian |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Blast |b [an essential guide to the basic local alignment search tool] |c Ian Korf, Mark Yandell, and Joseph Bedell |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Beijing [u.a.] |b O'Reilly |c 2003 | |
| 300 | |a XVIII, 339 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 630 | 0 | 4 | |a BLAST (Computer file) |
| 630 | 0 | 7 | |a BLAST |0 (DE-588)4748430-5 |2 gnd |9 rswk-swf |
| 650 | 4 | |a BLAST | |
| 650 | 4 | |a Datenverarbeitung | |
| 650 | 4 | |a Amino acid sequence |x Databases | |
| 650 | 4 | |a Biology |x Data processing | |
| 650 | 4 | |a Database searching | |
| 650 | 4 | |a Nucleotide sequence |x Databases | |
| 689 | 0 | 0 | |a BLAST |0 (DE-588)4748430-5 |D u |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Yandell, Mark |e Verfasser |4 aut | |
| 700 | 1 | |a Bedell, Joseph |e Verfasser |4 aut | |
| 856 | 4 | 2 | |m DNB Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010574724&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-010574724 | |
Datensatz im Suchindex
| _version_ | 1808044694220832768 |
|---|---|
| adam_text |
TABLE
OF
CONTENTS
FOREWORD
.
XI
PREFACE
.
XIII
PART
I.
INTRODUCTION
1.
HELLO
BLAST
.
3
WHAT
IS
BLAST?
3
USING
NCBI-BLAST
4
ALTERNATE
OUTPUT
FORMATS
12
ALTERNATE
ALIGNMENT
VIEWS
13
THE
NEXT
STEP
14
FURTHER
READING
15
PART
II.
THEORY
2.
BIOLOGICAL
SEQUENCES
.19
THE
CENTRAL
DOGMA
OF
MOLECULAR
BIOLOGY
19
EVOLUTION
27
GENOMES
AND
GENES
35
BIOLOGICAL
SEQUENCES
AND
SIMILARITY
38
FURTHER
READING
39
3.
SEQUENCE
ALIGNMENT
.
40
GLOBAL
ALIGNMENT:
NEEDLEMAN-WUNSCH
40
LOCAL
ALIGNMENT:
SMITH-WATERMAN
46
DYNAMIC
PROGRAMMING
50
ALGORITHMIC
COMPLEXITY
50
GLOBAL
VERSUS
LOCAL
50
VARIATIONS
51
FINAL
THOUGHTS
53
FURTHER
READING
53
4.
SEQUENCE
SIMILARITY
.
55
INTRODUCTION
TO
INFORMATION
THEORY
55
AMINO
ACID
SIMILARITY
57
SCORING
MATRICES
59
TARGET
FREQUENCIES,
LAMBDA,
AND
H
60
SEQUENCE
SIMILARITY
64
KARLIN-ALTSCHUL
STATISTICS
65
SUM
STATISTICS
AND
SUM
SCORES
67
FURTHER
READING
70
PART
III.
PRACTICE
5.
BLAST
.
75
THE
FIVE
BLAST
PROGRAMS
75
THE
BLAST
ALGORITHM
76
FURTHER
READING
87
6.
ANATOMY
OF
A
BLAST
REPORT
.
88
BASIC
STRUCTURE
88
ALIGNMENTS
90
7.
A
BLAST
STATISTICS
TUTORIAL
.
96
BASIC
BLAST
STATISTICS
96
USING
STATISTICS
TO
UNDERSTAND
BLAST
RESULTS
109
WHERE
DID
MY
OLIGO
GO?
109
8.
20
TIPS
TO
IMPROVE
YOUR
BLAST
SEARCHES
.
116
8.1
DON
'
T
USE
THE
DEFAULT
PARAMETERS
116
8.2
TREAT
BLAST
SEARCHES
AS
SCIENTIFIC
EXPERIMENTS
116
8.3
PERFORM
CONTROLS,
ESPECIALLY
IN
THE
TWILIGHT
ZONE
117
VI
|
TABLE
OF
CONTENTS
8.4
VIEW
BLAST
REPORTS
GRAPHICALLY
118
8.5
USE
THE
KARLIN-ALTSCHUL
EQUATION
TO
DESIGN
EXPERIMENTS
119
8.6
WHEN
TROUBLESHOOTING,
READ
THE
FOOTER
FIRST
119
8.7
KNOW
WHEN
TO
USE
COMPLEXITY
FILTERS
120
8.8
MASK
REPEATS
IN
GENOMIC
DNA
121
8.9
SEGMENT
LARGE
GENOMIC
SEQUENCES
121
8.10
BE
SKEPTICAL
OF
HYPOTHETICAL
PROTEINS
123
8.11
EXPECT
CONTAMINANTS
IN
EST
DATABASES
123
8.12
USE
CAUTION
WHEN
SEARCHING
RAW
SEQUENCING
READS
124
8.13
LOOK
FOR
STOP
CODONS
AND
FRAME-SHIFTS
TO
FIND
PSEUDO-GENES
124
8.14
CONSIDER
USING
UNGAPPED
ALIGNMENT
FOR
BLASTX,
TBLASTN,
AND
TBLASTX
124
8.15
LOOK
FOR
GAPS
IN
COVERAGE
AS
A
SIGN
OF
MISSED
EXONS
126
8.16
PARSE
BLAST
REPORTS
WITH
BIOPERL
126
8.17
PERFORM
PILOT
EXPERIMENTS
128
8.18
EXAMINE
STATISTICAL
OUTLIERS
128
8.19
USE
LINKS
AND
TOPCOMBON
TO
MAKE
SENSE
OF
ALIGNMENT
GROUPS
128
8.20
HOW
TO
LIE
WITH
BLAST
STATISTICS
128
9.
BLAST
PROTOCOLS
.
130
BLASTN
PROTOCOLS
131
BLASTP
PROTOCOLS
144
BLASTX
PROTOCOLS
147
TBLASTN
PROTOCOLS
152
TBLASTX
PROTOCOLS
155
PART
IV.
INDUSTRIAL-STRENGTH
BLAST
10.
INSTALLATION
AND
COMMAND-LINE
TUTORIAL
.
161
NCBI-BLAST
INSTALLATION
161
WU-BLAST
INSTALLATION
166
COMMAND-LINE
TUTORIAL
170
EDITING
SCORING
MATRICES
186
TABLE
OF
CONTENTS
|
VII
11.
BLAST
DATABASES
.
188
FAST
A
FILES
188
BLAST
DATABASES
193
SEQUENCE
DATABASES
198
SEQUENCE
DATABASE
MANAGEMENT
STRATEGIES
206
12.
HARDWARE
AND
SOFTWARE
OPTIMIZATIONS
.
213
THE
PERSISTENCE
OF
MEMORY
213
CPUS
AND
COMPUTER
ARCHITECTURE
215
COMPUTE
CLUSTERS
216
DISTRIBUTED
RESOURCE
MANAGEMENT
218
SOFTWARE
TRICKS
220
OPTIMIZED
NCBI-BLAST
224
PART
V.
BLAST
REFERENCE
13.
NCBI-BLAST
REFERENCE
.
229
USAGE
STATEMENTS
229
COMMAND-LINE
SYNTAX
229
BIASTAIL
PARAMETERS
230
FORMATDB
PARAMETERS
240
FASTACMD
PARAMETERS
242
MEGABLAST
PARAMETERS
245
BL2SEQ
PARAMETERS
252
BLASTPGP
PARAMETERS
(PSI-BLAST
AND
PHI-BLAST)
256
BLASTCLUST
PARAMETERS
264
14.
WU-BLAST
REFERENCE
.
267
USAGE
STATEMENTS
268
COMMAND-LINE
SYNTAX
268
WU-BLAST
PARAMETERS
269
XDFORMAT
PARAMETERS
281
XDGET
PARAMETERS
285
VIII
|
TABLE
OF
CONTENTS
PART
VI.
APPENDIXES
A.
NCBI
DISPLAY
FORMATS
.
291
B.
NUCLEOTIDE
SCORING
SCHEMES
.
299
C
NCBI-BLAST
SCORING
SCHEMES
.
302
D.
BLAST-IMAGER.PL
.
305
E.
BLAST2TABLE.PL
.
309
GLOSSARY
.
313
INDEX
.
319
TABLE
OF
CONTENTS
|
IX |
| any_adam_object | 1 |
| author | Korf, Ian Yandell, Mark Bedell, Joseph |
| author_facet | Korf, Ian Yandell, Mark Bedell, Joseph |
| author_role | aut aut aut |
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| author_variant | i k ik m y my j b jb |
| building | Verbundindex |
| bvnumber | BV017574694 |
| callnumber-first | Q - Science |
| callnumber-label | QH324 |
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| callnumber-search | QH324.2 |
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| callnumber-subject | QH - Natural History and Biology |
| classification_rvk | WC 7700 |
| classification_tum | BIO 180f DAT 660f BIO 110f |
| ctrlnum | (OCoLC)249378448 (DE-599)BVBBV017574694 |
| dewey-full | 572.80285536 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.80285536 |
| dewey-search | 572.80285536 |
| dewey-sort | 3572.80285536 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Informatik |
| edition | 1. ed. |
| format | Book |
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| id | DE-604.BV017574694 |
| illustrated | Illustrated |
| indexdate | 2024-08-22T00:16:26Z |
| institution | BVB |
| isbn | 0596002998 9780596002992 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-010574724 |
| oclc_num | 249378448 |
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| physical | XVIII, 339 S. graph. Darst. |
| publishDate | 2003 |
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| spelling | Korf, Ian Verfasser aut Blast [an essential guide to the basic local alignment search tool] Ian Korf, Mark Yandell, and Joseph Bedell 1. ed. Beijing [u.a.] O'Reilly 2003 XVIII, 339 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier BLAST (Computer file) BLAST (DE-588)4748430-5 gnd rswk-swf BLAST Datenverarbeitung Amino acid sequence Databases Biology Data processing Database searching Nucleotide sequence Databases BLAST (DE-588)4748430-5 u DE-604 Yandell, Mark Verfasser aut Bedell, Joseph Verfasser aut DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010574724&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Korf, Ian Yandell, Mark Bedell, Joseph Blast [an essential guide to the basic local alignment search tool] BLAST (Computer file) BLAST (DE-588)4748430-5 gnd BLAST Datenverarbeitung Amino acid sequence Databases Biology Data processing Database searching Nucleotide sequence Databases |
| subject_GND | (DE-588)4748430-5 |
| title | Blast [an essential guide to the basic local alignment search tool] |
| title_auth | Blast [an essential guide to the basic local alignment search tool] |
| title_exact_search | Blast [an essential guide to the basic local alignment search tool] |
| title_full | Blast [an essential guide to the basic local alignment search tool] Ian Korf, Mark Yandell, and Joseph Bedell |
| title_fullStr | Blast [an essential guide to the basic local alignment search tool] Ian Korf, Mark Yandell, and Joseph Bedell |
| title_full_unstemmed | Blast [an essential guide to the basic local alignment search tool] Ian Korf, Mark Yandell, and Joseph Bedell |
| title_short | Blast |
| title_sort | blast an essential guide to the basic local alignment search tool |
| title_sub | [an essential guide to the basic local alignment search tool] |
| topic | BLAST (Computer file) BLAST (DE-588)4748430-5 gnd BLAST Datenverarbeitung Amino acid sequence Databases Biology Data processing Database searching Nucleotide sequence Databases |
| topic_facet | BLAST (Computer file) BLAST Datenverarbeitung Amino acid sequence Databases Biology Data processing Database searching Nucleotide sequence Databases |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010574724&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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