What is BLAST? Basic BLAST search What is BLAST?

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Presentation transcript:

What is BLAST? Basic BLAST search What is BLAST? The framework of BLAST Different BLAST programs BLAST databases you can search Where can I run BLAST?

What is BLAST? BLAST stands for Why BLAST is popular? 12/08/2014 What is BLAST? BLAST stands for Basic Local Alignment Search Tool Why BLAST is popular? Good balance of sensitivity and speed Reliable Flexible Local alignments; short significant stretches of similarity, irrespective of where they are in the sequence Blast applies heuristic approach, it does not necessarily find the best hit for your search. Statistical standpoint and software development point It can be adapted to many sequence analysis scenarios.

The most common BLAST search includes five programs: BLAST Programs The most common BLAST search includes five programs: Program Database (Subject) Query BLASTN Nucleotide BLASTP Protein BLASTX Nt.  Protein TBLASTN TBLASTX

BLASTN BLASTN DNA :: DNA homology The query is a nucleotide sequence 12/08/2014 BLASTN BLASTN The query is a nucleotide sequence The database is a nucleotide database No conversion is done on the query or database DNA :: DNA homology Mapping oligos to a genome Annotating genomic DNA with ESTs Annotating untranslated regions

BLASTP BLASTP Protein :: Protein homology 12/08/2014 BLASTP BLASTP The query is an amino acid sequence The database is an amino acid database No conversion is done on the query or database Protein :: Protein homology Protein function exploration Novel gene  make parameters more sensitive Score matrix, e value, parameter

BLASTX BLASTX Coding nucleotide seq :: Protein homology The query is a nucleotide sequence The database is an amino acid database All six reading frames are translated on the query and used to search the database Coding nucleotide seq :: Protein homology Gene finding in genomic DNA Annotating ESTs (and shotgun sequences)

TBLASTN TBLASTN The query is an amino sequence The database is a nucleotide database All six frames are translated in the database and searched with the protein sequence Protein :: Coding nucleotide DB homology Mapping a protein to a genome Mining ESTs (shotgun sequences) for protein similarities

TBLASTX TBLASTX The query is a nucleotide sequence The database is a nucleotide database All six frames are translated on the query and on the database Coding :: Coding homology Searching distantly-related species Sensitive but expensive

BLAST output List of sequences with scores Raw score Higher is better Depends on aligned length Expect Value (E-value) Smaller is better Independent of length and database size List of alignments

The Databases (1) GenBank NR (protein and nucleotide versions) Non-redundant large databases (compile and remove duplicates) Anyone can submit, you can call your sequence anything Low quality; names can be meaningless EST databases Short single reads of cDNA clones Short single reads High error rates

The Databases (2) UniProt/Swiss-Prot Curated from literature REAL proteins; REAL functions; small; Genomic databases Human, Mouse, Drosophila, Arabidopsis, etc. NCBI, species-specific web pages

Where Can I run BLAST? NCBI BLAST web service https://blast.ncbi.nlm.nih.gov/Blast.cgi EBI BLAST web service http://www.ebi.ac.uk/Tools/sss/ncbiblast/ FlyBase BLAST http://flybase.org/blast/ Drosophila and other insects