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BLAST(Basic Local Alignment Tool)
The document discusses the Basic Local Alignment Search Tool (BLAST), a set of algorithms for comparing gene and protein sequences against public databases. It highlights BLAST's efficiency over traditional alignment methods, particularly its speed, and provides an overview of its functionality and various types of BLAST programs. The exponential growth of sequence data and the importance of rapid similarity searching for better understanding of sequences are emphasized.
BLAST(Basic Local Alignment Tool)
- 1. Any important workthat does not begin with Bismillah is imperfect.
- 3. (Basic local alignmentsearch Tool) Fast similarity searching of the database
- 4. Definition & DescriptionBackground Algorithm Types of BLAST program BLAST search BLAST Functions
- 6. The Basic LocalAlignment Search Tool ( BLAST ) for comparing gene and protein sequences against others in public databases.
- 7. Fasta Ssearch BLASTWU-BLAST ?? ?? ??
- 8. 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. It breaks the query and database sequences into fragments and seeks matches between them.
- 9. When you havea nucleotide or protein sequence that you want to search against sequence databases to determine what the sequence is to find related sequences (homologs) For Better Understanding let’s take a look at alignment background
- 11. 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. Amazingly, this sequence data doubles every 18 months!
- 12. Today, one ofthe 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). BLAST is a computer algorithm that is available for use online at the (National Center for Biotechnology Information (NCBI) website and many other sites
- 13. Nucleic acid /ProteinAlignments were time consuming. Alignments were done by full alignment by using dynamic programming . BLAST is 50 times faster then dynamic programming.
- 16. 1- The Smith-Waterman Algorithm 2- BLAST
- 17. Assign penalties to mismatched pairs, insertions and deletions. Rather than (global alignment), the SW examines all sub-sequences found within the query and potential match sequences, returning only the highest scoring alignment.
- 18. BLAST uses analgorithm very similar to the Smith-Waterman to query databases for best sequence similarity matches. Heuristic algorithm Advantage: Speed Disadvantage: Deterministic algorithms only return one “best” alignment. There may be many alignments with high scores that won’t be found with this approach.
- 19. Main idea: Constructa dictionary of all the words in the query Initiate a local alignment for each word match between query and DB query DB
- 20. First step: Foreach position p of the query, find the list or words of length w scoring more than T when paired with the word starting at p: p-word List of all words of length w, scoring more than T with the p-word.
- 21. Extension of hits:requires a second hit on the same diagonal.
- 22. Gapped extension ofHigh Scoring Pairs above a threshold.
- 23. Input and outputconform to the FASTA format
- 25. 1- Nucleotide-nucleotide BLAST (blastn) 2- Protein-protein BLAST (blastp) 3- Position-Specific Iterative BLAST (PSI-BLAST) 4- Nucleotide 6-frame translation-protein (blastx) 5- Nucleotide 6-frame translation-nucleotide 6-frame translation (tblastx) 6- Protein-nucleotide 6-frame translation (tblastn) 7- Large numbers of query sequences (megablast)
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- 31. Select a BLASTprogram Selecting the BLAST Database Entering your Sequence FASTA format Accession / GI number Submitting your search
- 33. Insert your sequencein FASTA format Submit your search
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- 36. Identifying Species LocatingDomains Establishing Phylogeny DNA Mapping Comparison
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