BLAST [Basic Alignment Local Search Tool]
Upcoming SlideShare
Loading in...5
×
 

BLAST [Basic Alignment Local Search Tool]

on

  • 513 views

 

Statistics

Views

Total Views
513
Views on SlideShare
289
Embed Views
224

Actions

Likes
0
Downloads
31
Comments
0

1 Embed 224

http://epembelajaran.umt.edu.my 224

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

    BLAST [Basic Alignment Local Search Tool] BLAST [Basic Alignment Local Search Tool] Presentation Transcript

    • BLAST
    • BLAST Basic Local Alignment Search ToolNational Center for Biotechnology Information (NCBI)Fundamental The search revealsways of learning what relatedabout a protein sequences areor gene present in the same organism and other organisms.
    • BLAST Typically, this means that millions of alignments are analyzed in a BLAST search, and only the most closely related matches are returned. Query sequenceNeedleman–Wunsch (1970)Because we are usually more Target Sequenceinterested in identifying locallymatching regions such asprotein domains.
    • BLAST Typically, this means that millions of alignments are analyzed in a BLAST search, and only the most closely related matches are returned. Query sequence Smith–Waterman (1981)we cannot generally use it for Target Sequencedatabase searches because it istoo computationally intensive.
    • BLAST Typically, this means that millions of alignments are analyzed in a BLAST search, and only the most closely related matches are returned. Query sequence BLASToffers a local alignment Target Sequencestrategy having both speed andsensitivity. It also offersconvenient accessibility on theWorldWideWeb.
    • BLAST Target Sequence Query sequenceA DNA sequence can The programs Family produce high-be converted intosix potential scoring segmentproteins, and the pairs (HSPs) thatBLAST algorithms represent localinclude strategies to alignments betweencompare protein your query andsequences to databasedynamically sequences.translated DNAdatabases or viceversa. Programs
    • 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
    • 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.
    • 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 BLAST search.
    • BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastp protein proteinUse blastp to compare a protein query to a database of proteins 1Blastn DNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6Blastx DNA 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 6tBlastn protein 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 DNA DNATblastx 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.
    • BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastp protein proteinUse blastp to compare a protein query to a database of proteins 1Blastn DNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6Blastx DNA 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 6tBlastn protein 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 DNA DNATblastx 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.
    • BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastp protein proteinUse blastp to compare a protein query to a database of proteins 1Blastn DNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6Blastx DNA 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 6tBlastn protein 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 DNA DNATblastx 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.
    • BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastp protein proteinUse blastp to compare a protein query to a database of proteins 1Blastn DNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6Blastx DNA 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 6tBlastn protein 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 DNA DNATblastx 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.
    • BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastp protein proteinUse blastp to compare a protein query to a database of proteins 1Blastn DNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6Blastx DNA 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 6tBlastn protein 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 DNA DNATblastx 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.
    • BLAST SEARCH STEPS 1. Step 2: Selecting BLAST ProgramProgram Query Number of database searches Database 1Blastp protein proteinUse blastp to compare a protein query to a database of proteins 1Blastn DNA DNAUse blastn to compare both strands of a DNA query against a DNA database. 6Blastx DNA 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 6tBlastn protein 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 DNA DNATblastx 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.
    • Subscribe