BLAST(Basic Local Alignment Tool)


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The Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against others in public databases.

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BLAST(Basic Local Alignment Tool)

  1. 1. Any important work that does not begin with Bismillah is imperfect.
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  3. 3. (Basic local alignment search Tool) Fast similarity searching of the database
  4. 4. <ul><li>Definition & Description </li></ul><ul><li>Background </li></ul><ul><li>Algorithm </li></ul><ul><li>Types of BLAST program </li></ul><ul><li>BLAST search </li></ul><ul><li>BLAST Functions </li></ul>
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  6. 6. <ul><li>The Basic Local Alignment Search Tool ( BLAST ) for comparing gene and protein sequences against others in public databases. </li></ul>
  7. 7. <ul><li>Fasta </li></ul><ul><li>Ssearch </li></ul><ul><li>BLAST </li></ul><ul><li>WU-BLAST </li></ul>?? ?? ??
  8. 8. <ul><li>BLAST – B asic L ocal A lignment S earch T ool is a set of sequence comparison algorithms used to search databases for optimal local alignments to a query. </li></ul><ul><li>It breaks the query and database sequences into fragments and seeks matches between them. </li></ul>
  9. 9. <ul><li>When you have a nucleotide or protein sequence that you want to search against sequence databases </li></ul><ul><ul><li>to determine what the sequence is </li></ul></ul><ul><ul><li>to find related sequences (homologs) </li></ul></ul>For Better Understanding let’s take a look at alignment background
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  11. 11. <ul><li>Beginning in the 1970s , scientists began to accumulate DNA and protein sequence data at an exponential rate; in fact, researchers currently have approximately 97 billion bases sequenced and over 93 million records. </li></ul><ul><li>Amazingly, this sequence data doubles every 18 months! </li></ul>
  12. 12. <ul><li>Today, one of the most commonly used tools to examine DNA and protein sequences is the Basic Local Alignment Search Tool, also known as BLAST (Altschul et al ., 1990). </li></ul><ul><li>BLAST is a computer algorithm that is available for use online at the (National Center for Biotechnology Information (NCBI) website and many other sites </li></ul>
  13. 13. <ul><li>Nucleic acid /Protein Alignments were time consuming. </li></ul><ul><li>Alignments were done by full alignment by using dynamic programming . </li></ul><ul><li>BLAST is 50 times faster then dynamic programming. </li></ul>
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  16. 16. <ul><li>1- The Smith -Waterman Algorithm </li></ul><ul><li>2- BLAST </li></ul>
  17. 17. <ul><li>Assign penalties to mismatched pairs, insertions and deletions. </li></ul><ul><li>Rather than (global alignment), the SW examines all sub-sequences found within the query and potential match sequences, returning only the highest scoring alignment. </li></ul>
  18. 18. <ul><li>BLAST uses an algorithm very similar to the Smith-Waterman to query databases for best sequence similarity matches. </li></ul><ul><li>Heuristic algorithm </li></ul><ul><li>Advantage: Speed </li></ul><ul><li>Disadvantage: Deterministic algorithms only return one “best” alignment. There may be many alignments with high scores that won’t be found with this approach. </li></ul>
  19. 19. <ul><li>Main idea: </li></ul><ul><li>Construct a dictionary of all the words in the query </li></ul><ul><li>Initiate a local alignment for each word match between query and DB </li></ul>query DB
  20. 20. <ul><li>First step: </li></ul><ul><li>For each position p of the query, find the list or words of length w </li></ul><ul><li>scoring more than T when paired with the word starting at p: </li></ul>p-word List of all words of length w, scoring more than T with the p-word.
  21. 21. <ul><li>Extension of hits: requires a second hit on the same diagonal. </li></ul>
  22. 22. <ul><li>Gapped extension of High Scoring Pairs above a threshold. </li></ul>
  23. 23. <ul><li>Input and output conform to the </li></ul><ul><li>FASTA format </li></ul>
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  25. 25. <ul><li>1- Nucleotide-nucleotide BLAST (blastn) </li></ul><ul><li>2- Protein-protein BLAST (blastp) </li></ul><ul><li>3- Position-Specific Iterative BLAST (PSI-BLAST) </li></ul><ul><li>4- Nucleotide 6-frame translation-protein (blastx) </li></ul><ul><li>5- Nucleotide 6-frame translation-nucleotide 6-frame translation (tblastx) </li></ul><ul><li>6- Protein-nucleotide 6-frame translation (tblastn) </li></ul><ul><li>7- Large numbers of query sequences (megablast) </li></ul>
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  30. 31. <ul><li>Select a BLAST program </li></ul><ul><li>Selecting the BLAST Database </li></ul><ul><li>Entering your Sequence </li></ul><ul><ul><li>FASTA format </li></ul></ul><ul><ul><li>Accession / GI number </li></ul></ul><ul><li>Submitting your search </li></ul>
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  32. 33. Insert your sequence in FASTA format Submit your search
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  34. 36. <ul><li>Identifying Species </li></ul><ul><li>Locating Domains </li></ul><ul><li>Establishing Phylogeny </li></ul><ul><li>DNA Mapping </li></ul><ul><li>Comparison </li></ul>
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