BLAT ndash; The BLAST-Like Alignment Tool.ppt

BLAT – The BLAST-Like Alignment Tool Kent, W.J. Genome Res. 2002 12: 656-664 Presenter: 巨彥霖 田知本 BLAT overview Use an index to find regions in genome homologous to query. Do a detailed alignment between query and homologous regions. Use dynamic programming to stitch together detailed alignments regions into detailed alignment of whole. Index Database : non-overlapping Query : overlapping Example Database: cacaattatcacgaccgc 3-mers: cac aat tat cac gac cgc Index: aat 3 gac 12 cac 0,9 tat 6 cgc 15 Query: aattctcac 3-mers: aat att ttc tct ctc tca cac 0 1 2 3 4 5 6 Search Criteria Single Perfect Matches Single Near Perfect Matches Multiple Perfect Matches Notation K : K-mer size M : The match ratio between homologous area H : Homologous region size G : Query sequence size A : The alphabet size Single Perfect Matches (1) Single Perfect Matches (2) Single Perfect Matches (3) The number of k-mer in the database = G / K The number of k-mer in the query = Q – K + 1 ? The number of k-mer that are expected to matched by chance : ? Case (perfect match) Comparing mouse and human coding sequences at the nucleotide level : H = 100 M = 86% Sensitivity = 0.99 ? max K = 7 chance matches = (query = 500 , database = 3 billion) Single Near Perfect Matches (1) Single Near Perfect Matches (2) Sensitivity Specificity ? Case (near perfect match) Comparing mouse and human coding sequences at the nucleotide level : H = 100 M = 86% Sensitivity = 0.99 ? max K = 12 chance matches = 275671 (query = 500 , database = 3 billion) Multiple Perfect Matches Hit is triggered : there must be N perfect matches each no further than W letters from each other in the database coordinate have the same diagonal coordinate Example Default Nucleotide two perfect 11-mer Protein single perfect