BLAST

NCBI Home NCBI Site Map      brief/complete Course Description Schedule Introduction Genetics Review Types of Databases Format of Sequence Record Entrez BLAST 3-D Structures Genomes and Maps Librarian Roles WWW Sites Glossaries and Dictionaries

Sequence Similarity Searches Basic Local Alignment Search Tool query is a DNA or protein sequence in FASTA format, not a text term character string comparison against all the sequences in the target database rigorous statistics used to identify statistically significant matches BLAST programs BLAST databases Jurassic Park dinosaur sequence appears on page 103 of Jurassic Park, by Michael Crichton (Ballantyne Books, 1993) FASTA format BLAST search Try a blastn search using this sequence against the nucleotide non-redundant (nr) database to find out what the sequence might be. BLAST search results BioTechniques publication by Mark Boguski The Lost World another book... The Lost World, by Michael Crichton (Ballantyne Books, 1996) another sequence...(page 135) FASTA format BLAST search Try another blastn search using this new sequence against the nucleotide non-redundant (nr) database to find out what it might be. BLAST search results BLAST search again, with a twist... Try one more BLAST search, this time using the blastx program, to compare the protein translation of the dinosaur sequence against the protein non-redundant (nr) database. Look at the pairwise alignments for the first few hits. See anything strange about the amino acid residues in the gaps of the alignment? Mark Boguski strikes again... BLAST search results and pairwise alignment of protein query and closest hit Ataxia Telangiectasia the hunt for the ataxia telangiectasia gene Reference:  Boguski, M.S. 1995. Molecular medicine: Hunting for genes in computer DNA data bases. New England Journal of Medicine 333:645-647. [PubMed] Neurofibromatosis (NF1) Reference: Ballester R, Marchuk D, Boguski M, Saulino A, Letcher R, Wigler M, Collins F. 1990. The NF1 locus encodes a protein functionally related to mammalian GAP and yeast IRA proteins. Cell. Nov 16;63(4):851-9. [PubMed] More on BLAST searching... Scoring matrices identity matrix for nucleotides substitution matrices for proteins, e.g., Blosum62 PAM 30 (Percent Accepted Mutation) Position Specific Other versions of BLAST PSI BLAST PHI BLAST BLAST 2 Sequences BLAST against microbial genomes BLAST against human chromosomes Exercises BLAST tutorial Try a Coffee Break! References BLAST Introduction Baxevanis, A.D., M.S. Boguski, B.F.F. Ouellette. 1997. Computational analysis of DNA and protein sequences. Chapter 7 IN Analyzing DNA, Volume 1 of Genome Analysis: A Laboratory Manual Series. New York: Cold Spring Harbor Laboratory Press. Accessible by linking directly to: http://www.cshl.org/books/g_a/indxbk1.htm Schuler, G.D. 1998. Sequence Alignment and Database Searching. Chapter 7 IN Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, edited by Baxevanis, A. and Ouellette, B.F.F. New York: John Wiley & Sons BLAST Help Documentation Accessible from the BLAST WWW page, or from the BLAST e-mail server (blast@ncbi.nlm.nih.gov) by sending the word HELP in the body of a message to the server address. FAQs are also accessible from the BLAST WWW page. Articles: See articles cited on the various BLAST pages.

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Revised March 30, 2001 Comments/questions about course to Renata Geer renata@ncbi.nlm.nih.gov Questions about NCBI resources to info@ncbi.nlm.nih.gov