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Blast: [an essential guide to the basic local alignment search tool]

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Bibliographic Details
Main Authors:	Korf, Ian (Author), Yandell, Mark (Author), Bedell, Joseph (Author)
Format:	Book
Language:	English
Published:	Beijing [u.a.] O'Reilly 2003
Edition:	1. ed.
Subjects:	BLAST (Computer file) BLAST Datenverarbeitung Amino acid sequence > Databases Biology > Data processing Database searching Nucleotide sequence > Databases
Online Access:	Inhaltsverzeichnis
Physical Description:	XVIII, 339 S. graph. Darst.
ISBN:	0596002998 9780596002992

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MARC


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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
author_sort	Korf, Ian
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
callnumber-sort	QH 3324.2
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
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oclc_num	249378448
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physical	XVIII, 339 S. graph. Darst.
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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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