book

BLAST

by Ian Korf, Mark Yandell, Joseph Bedell

July 2003

Intermediate to advanced

368 pages

13h 44m

English

O'Reilly Media, Inc.

Read now

Unlock full access

Audience for This Book
Conventions Used in This BookURLs Referenced in This BookComments and Questions
IanMarkJoey
What Is BLAST?
Choosing the BLAST ProgramEntering the Query SequenceChoosing the Database to SearchChoosing the Parameters of the SearchChoosing the FormatSubmitting the SearchViewing the Results

The Central Dogma of Molecular BiologyDNARNAProtein
MutationNatural SelectionGenetic DriftThe Neutral Theory of Evolution
Molecular ClocksHomology, Phylogeny, and TreesThe Tree of Life
Prokaryotic GenesEukaryotic GenesTranscriptsRepeats
Biological Sequences and Similarity
Global Alignment: Needleman-WunschInitializationFillTrace-Back
Algorithmic ComplexityGlobal Versus Local
Gap ModificationsReduced Memory
Final ThoughtsFurther Reading
Introduction to Information Theory
Target Frequencies, lambda, and HLambdaRelative EntropyMatch-Mismatch Scoring
Gapped AlignmentsLength Correction
Converting a Sum Score to a Sum Probability
Further Reading
The Five BLAST Programs
SeedingImplementation details
ExtensionImplementation detailsEvaluation
Implementation details
Basic Structure
BLASTPBLASTNBLASTXTBLASTNTBLASTXAlignment Groups
Basic BLAST StatisticsActual Versus Effective LengthsThe Raw Score and Bit Score
The WU-BLAST P-ValueSum StatisticsAn Expect(n) Means That Sum Statistics Were AppliedSum Statistics Are Pair-Wise in Their FocusThe Sum ScoreEffective Length of a BLASTX Query
Calculating the Pair-Wise Sum P-ValueCorrecting for Multiple TestsCorrecting for Database SizeFrame- and Size-Corrected Expects
Where Did My Oligo Go?Karlin-Altschul Statistics as a Tool for Further Investigation
8.1 Don’t Use the Default Parameters8.2 Treat BLAST Searches as Scientific Experiments
8.6 When Troubleshooting, Read the Footer First
8.9 Segment Large Genomic Sequences
8.11 Expect Contaminants in EST Databases
8.13 Look for Stop Codons and Frame-Shifts to find Pseudo-Genes8.14 Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX
8.16 Parse BLAST Reports with Bioperl
8.18 Examine Statistical Outliers8.19 Use links and topcomboN to Make Sense of Alignment Groups8.20 How to Lie with BLAST Statistics
Mapping Oligos to a GenomeApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsMapping Nonspliced DNA to a GenomeApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsMapping a cDNA/EST to a GenomeApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsCross-Species Sequence ExplorationApproachNCBI-BLAST parameters
WU-BLAST parametersExpected resultsOptimizations and variationsAnnotating Genomic DNA with ESTsApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsTranscript Clustering and ExtensionApproachNCBI-BLAST parametersWU-BLAST parametersExpected results
Clustering with blastclustApproachEST clusteringShotgun sequencesExpected resultsVector ClippingApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsRepeat MaskingApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variations
BLASTP ProtocolsThe Standard BLASTP SearchApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsFast, Insensitive SearchApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsSlow, Sensitive SearchApproach
WU-BLAST parametersExpected resultsOptimizations and variationsBLASTX ProtocolsGene Finding in Genomic DNAApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsAnnotating ESTs (and Shotgun Sequence)ApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsSuper-Fast BLASTXApproach
WU-BLAST parametersWU-BLAST 1.4 parametersExpected resultsOptimizations and variationsTBLASTN ProtocolsMapping a Protein to a GenomeApproachNCBI-BLAST parametersWU-BLAST parametersExpected resultsOptimizations and variationsMining ESTs (and Shotgun DNA) for Protein SimilaritiesApproachNCBI-BLAST parametersWU-BLAST parameters
Optimizations and variationsTBLASTX ProtocolsPreventing Stop CodonsFinding Undocumented Genes in Genomic DNAApproachNCBI-BLASTWU-BLASTExpected resultsOptimizations and variationsTranscript-Transcript TBLASTXApproachNCBI-BLASTWU-BLASTExpected resultsOptimizations and variations
NCBI-BLAST InstallationUnix InstallationFiles and directoriesThe .ncbirc fileSetting the PATH and BLASTDB environment variablesWindows InstallationThe ncbi.ini fileSetting the PATH environment variableMacintosh OS X Installation
WU-BLAST InstallationExpanding the tarballFiles and DirectoriesExecutablesEnvironment VariablesSetting Resource Limits with /etc/sysblast
NCBI-BLASTformatdbblastnmegablastblastpblastxtblastntblastx
bl2seqfastacmdPSI-BLASTPHI-BLASTEnvironment variables and .ncbirc
WU-BLASTxdformatblastnblastpblastxtblastntblastxxdget
nrdb and patdb
Editing Scoring Matrices
FASTA FilesNCBI Identifier FormatCompound identifiersConcatenated definition linesDescriptions
Large DatabasesLarge NCBI databasesLarge WU-BLAST databasesVirtual DatabasesAlias DatabasesRemoving RedundancyStandard BLAST Databases
Sequence Databases (1/2)International Nucleotide Sequence DatabaseDatabase GrowthFlat FilesACCESSION, LOCUS, VERSION, and GI
DEFINITION, KEYWORDS, and SOURCEFEATURESOther Common Databases
Queries, Indexes, and ReportsLocal Database ConsiderationsRetrieving FASTA Files by AccessionFlat File Indexing
Commercial Sequence Management SoftwareTools on the Internet
The Persistence of MemoryBLAST Pipelines and Caching
Operating Systems and CompilersCompute ClustersRemote Versus Local DatabasesRemote databases
Distributed Resource Management
Multiplexing/Query PackingQuery ChoppingDatabase SplittingSerial BLAST Searching
Apple/Genentech BLASTParacel-BLAST and BlastMachineTimeLogic Tera-BLAST
Usage StatementsCommand-Line Syntax
-a [integer]-A [integer]-b [integer]-B [integer]-d [database]-D [1..23]-e [real number]-E [integer]-f [integer]-F [T/F], -F [string]-g [T/F]-G [integer]-i [input file]-I [T/F]-J [T/F]-K [integer]
-l [file]-L [string]-m [0..11]-M [matrix file]-n [T/F]-o [output file]-p [program name]-P [0/1]-q [negative integer]-Q [1..23]-r [integer]-R [checkpoint file]-S [1..3]-t [integer]-T [T/F]-v [integer]-w [integer]-W [integer]-X [integer]-y [integer]-Y [real number]-z [real number]
formatdb Parameters-B [file]-F [file]-i [file]-l [file]-L [file]-n [string]-o [T/F]-p [T/F]
-t [string]-v [integer]-V [T/F]fastacmd Parameters-a [T/F]-c [T/F]-d [string]-D [T/F]-i [file]-I-l [integer]-L [integer],[integer]-o [file]-p [T/F/G]-P [integer]-s [string]
-t [T/F]-T [T/F]megablast Parameters (1/2)-a [integer]-A [integer]-b [integer]-d [string]-D [0..3]-e [real number]-E [integer]-f [T/F]-F [T/F] [string]-G [integer]-H [integer]-i [file]-I [T/F]-l [file]-L [string]-m [0..11]-M [integer]-n [T/F]-N [0,1,2]-o [file]
-p [real number]-P [integer]-q [negative integer]-Q [file]-r [integer]-R [T/F]-s [integer]-S [0..3]-t [16,18,21]-T [T/F]-U [T/F]-v [integer]-W [integer]-X [integer]-y [integer]
-Z [integer]bl2seq Parameters-a [file]-A [T/F]-d [real number]-D [0/1]-e [real number]-E [integer]-F [T/F] [string]-g [T/F]-G [integer]-i [file]-I [integer],[integer]-j [file]-J [integer],[integer]-m [T/F]-M [string]-o [file]-p [string]-q [negative integer]-r [integer]-S [1..3]-t [integer]-T [T/F]-U [T/F]-W [integer]-X [integer]-Y [real number]
PSI-BLASTPHI-BLAST-a [integer]-A [integer]-b [integer]-B [file]-c [integer]-C [file]-d [string]-e [real]-E [integer]-f [integer]-F [string]-g [T/F]-G [integer]-h [real number]-H [integer]-i [file]-I [T/F]
-j [integer]-J [T/F]-k [file]-K [integer]-l [string]-L [integer]-m [0..9]-M [string]-N [real number]-o [file]-O [file]-p [string]-Q [file]-R [file]-s [T/F]-S [integer]-t [T/F]-T [T/F]-U [T/F]-v [integer]
-X [integer]-y [real number]-Y [real number]-z [real number]-Z [integer]blastclust Parameters-a [integer]-b [T/F]-c [file]-C [T/F]-d [file]-e [T/F]-i [file]-l [file]-L [real number]-p [T/F]-r [file]-s [file]-v [file]-W [integer]
Command-Line Syntax
altscore=[string]B=[integer]bottomcpus=[integer]dbrecmax=[integer]dbrecmin=[integer]E=[number]E2=[number]echofiltererrorsfilter=[string]gapE2=[number]gapH=[number]gapK=[number]gapL=[number]gapS2=[integer]gapsepqmax=[int]gapsepsmax=[int]gapXgigolf=[number]golmax=[integer]gspmax=[integer]
H=[number]hspmax=[integer]hitdist=[integer]hspsepqmax=[int]hspsepsmax=[int]K=[number]kapL=[number]lcfilterlcmasklinksM=[integer]maskextra=[integer]matrix=[file]N=[integer]nogapnonnegoknosegsnotesnovalidctxoknwlen=[integer]nwstart=[integer]o=[file]olf=[number]olmax=[integer]postswQ=[integer]qoffset=[integer]qrecmax=[integer]Qrecmin=[integer]
R=[integer]restestS=[integer]mS2=[integer]seqtestspan, span1, span2T=[integer]toptopcomboN=[integer]V=[integer]warningswink=[integer]
W=[integer]X=[integer]Y=[number]Z=[number]xdformat Parameters-A [0..2]-a [database]-c [character]-D [integer]-d [string]-e [file]-G-i-K [integer]-k-L [number]-l [number]-M [number]-O [4..8]-P [integer]-q [0..3]-r-T [string]
-Xxdget Parameters-A [n, 0]-a [integer]-b [integer]-d-D [integer]-e [file]-F-f-G-o [file]-N [0, n]-P [integer]-r-T [string]-t
Brief DescriptionsDetailed Descriptions and ExamplesOption 0: Pairwise AlignmentsQuery-Anchored AlignmentsOption 1: Query-Anchored Showing IdentitiesOption 2: Query-Anchored, No IdentitiesOption 3: Flat Query-Anchored Showing IdentitiesOption 4: Flat Query-Anchored, No IdentitiesOption 5: Query-Anchored, No Identities, and Blunt EndsOption 6: Flat Query-Anchored, No Identities, and Blunt EndsOption 7: XMLOption 8: Tabular, Without Comment Lines
Option 10: ASN.1 Text FormatOption 11: ASN.1 Binary Format
NCBI-BLAST Matrices and Gap Costs