BLAST [Basic Alignment Local Search Tool]

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Transcript of BLAST [Basic Alignment Local Search Tool]

  • 1. BLAST

2. BLASTBasic Local Alignment Search ToolNational Center for Biotechnology Information (NCBI)Fundamental The search revealsways of learningwhat relatedabout a protein sequences areor gene present in the sameorganism and otherorganisms. 3. BLASTTypically, this means that millions of alignments are analyzed in a BLAST search, and only the most closely relatedmatches are returned. Query sequenceNeedlemanWunsch (1970)Because we are usually moreTarget Sequenceinterested in identifying locallymatching regions such asprotein domains. 4. BLASTTypically, this means that millions of alignments are analyzed in a BLAST search, and only the most closely relatedmatches are returned.Query sequenceSmithWaterman (1981)we cannot generally use it forTarget Sequencedatabase searches because it istoo computationally intensive. 5. BLASTTypically, this means that millions of alignments are analyzed in a BLAST search, and only the most closely relatedmatches are returned.Query sequence BLASToffers a local alignmentTarget Sequencestrategy having both speed andsensitivity. It also offersconvenient accessibility on theWorldWideWeb. 6. BLAST Target SequenceQuery sequenceA DNA sequence canThe programsFamilyproduce high-be converted intosix potential scoring segmentproteins, and the pairs (HSPs) thatBLAST algorithmsrepresent localinclude strategies to alignments betweencompare protein your query andsequences todatabasedynamically sequences.translated DNAdatabases or viceversa. Programs 7. BLAST1. Determining what orthologs and paralogs are known for a particular protein or nucleic acid sequence.2. Determining what proteins or genes are present in a particular organism.3. Determining the identity of a DNA or protein sequence.4. Discovering new genes.5. Determining what variants have been described for a particular gene or protein.6. Investigating expressed sequence tags that may exhibit alternative splicing.7. Exploring amino acid residues that are important in the function and/or structure of a protein 8. BLAST1. Selecting a sequence of interest and pasting, typing, or uploading it into the BLAST input box.2. Selecting a BLAST program (most commonly blastp, blastn, blastx, tblastx,blastn).3. Selecting a database to search. A common choice is the non redundant (nr) database, but there are many other databases.4. Selecting optional parameters, both for the search and for the format of the output. These options include choosing a substitution matrix, filtering of low complexity sequences, and restricting the search to a particular set of organisms. 9. BLAST SEARCH STEPS1. Step 1: Specifying Sequence of Interest: First Cutting and pasting DNA or protein sequence (e.g., in the FASTA format). Second using an accession number (e.g., a RefSeq or GenBank Identification [GI] number) BLAST searches, your query can be in uppercase or lowercase, with or without intervening spaces or numbers.If the query is DNA, BLAST algorithms will search both strands. It is often convenient to input the accession number to a BLASTsearch. 10. BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastpprotein proteinUse blastp to compare a protein query to a database of proteins 1BlastnDNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6BlastxDNA proteinBlastx translates a DNA sequence into six protein sequences using all six possiblereading frames, and then compares each of these proteins to a protein database 6tBlastnprotein DNATblastn is used to translate every DNA sequence in a database into six potentialproteins, and then to compare your protein query against each of those translated proteins. 36tBlastx DNADNATblastx is the most computational intensive BLAST algorithm. It translates DNA from both a query and a database into six potential proteins, and then performs 36 protein-protein database searches. 11. BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastpprotein proteinUse blastp to compare a protein query to a database of proteins 1BlastnDNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6BlastxDNA proteinBlastx translates a DNA sequence into six protein sequences using all six possiblereading frames, and then compares each of these proteins to a protein database 6tBlastnprotein DNATblastn is used to translate every DNA sequence in a database into six potentialproteins, and then to compare your protein query against each of those translated proteins. 36tBlastx DNADNATblastx is the most computational intensive BLAST algorithm. It translates DNA from both a query and a database into six potential proteins, and then performs 36 protein-protein database searches. 12. BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastpprotein proteinUse blastp to compare a protein query to a database of proteins 1BlastnDNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6BlastxDNA proteinBlastx translates a DNA sequence into six protein sequences using all six possiblereading frames, and then compares each of these proteins to a protein database 6tBlastnprotein DNATblastn is used to translate every DNA sequence in a database into six potentialproteins, and then to compare your protein query against each of those translated proteins. 36tBlastx DNADNATblastx is the most computational intensive BLAST algorithm. It translates DNA from both a query and a database into six potential proteins, and then performs 36 protein-protein database searches. 13. BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastpprotein proteinUse blastp to compare a protein query to a database of proteins 1BlastnDNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6BlastxDNA proteinBlastx translates a DNA sequence into six protein sequences using all six possiblereading frames, and then compares each of these proteins to a protein database 6tBlastnprotein DNATblastn is used to translate every DNA sequence in a database into six potentialproteins, and then to compare your protein query against each of those translated proteins. 36tBlastx DNADNATblastx is the most computational intensive BLAST algorithm. It translates DNA from both a query and a database into six potential proteins, and then performs 36 protein-protein database searches. 14. BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastpprotein proteinUse blastp to compare a protein query to a database of proteins 1BlastnDNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6BlastxDNA proteinBlastx translates a DNA sequence into six protein sequences using all six possiblereading frames, and then compares each of these proteins to a protein database 6tBlastnprotein DNATblastn is used to translate every DNA sequence in a database into six potentialproteins, and then to compare your protein query against each of those translated proteins. 36tBlastx DNADNATblastx is the most computational intensive BLAST algorithm. It translates DNA from both a query and a database into six potential proteins, and then performs 36 protein-protein database searches. 15. BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastpprotein proteinUse blastp to compare a protein query to a database of proteins 1BlastnDNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6BlastxDNA proteinBlastx translates a DNA sequence into six protein sequences using all six possiblereading frames, and then compares each of these proteins to a protein database 6tBlastnprotein DNATblastn is used to translate every DNA sequence in a database into six potentialproteins, and then to compare your protein query against each of those translated proteins. 36tBlastx DNADNATblastx is the most computational intensive BLAST algorithm. It translates DNA from both a query and a database into six potential proteins, and then performs 36 protein-protein database searches. 16. Subscribe