BLASTandMultipleSequenceAlignment.ppt

BLAST and Multiple Sequence Alignment Announcements Quiz #3 on Thurs., May 17 on lectures presented April 26, May 3 and May 15 Writing assignments due May 24 at the beginning of class. Learning objectives-Learn the basics of BLAST and Psi-BLAST and CLUSTAL W Workshop-Use of Psi-BLAST to determine sequence similarities. Homework-Due May 20 BLAST Basic Local Alignment Search Tool Speed is achieved by: Pre-indexing the database before the search Parallel processing Uses a hash table that contains neighborhood words. Neighborhood words The program declares a hit if the word taken from the query sequence has a score = T when a scoring matrix is used. This allows the word size (W) to be kept high (for speed) without sacrificing sensitivity. If T is increased user the number of background hits is reduced and the program will run faster. Which Program should one use? Most researchers use methods for determining local similarities: Smith-Waterman (gold standard) FASTA BLAST What are the different BLAST programs? blastp compares an amino acid query sequence against a protein sequence database blastn compares a nucleotide query sequence against a nucleotide sequence database blastx compares a nucleotide query sequence translated in all reading frames against a protein sequence database tblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames tblastx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that tblastx program cannot be used with the nr database on the BLAST Web page. Filtering Repetitive Sequences Over 50% of genomic DNA is repetitive This is due to: retrotransposons ALU region microsatellites centromeric sequences, telomeric sequences 5’ Untranslated Region of ESTs Filtering Repetitive Sequences (cont. 1) Programs like BLAST have the option of filtering out low complex regions. (Called Ma