Lecture 8: Bioinformatic Algorithms - Sequence Alignment and Suffix Trees, Study notes of Computer Science

Download Lecture 8: Bioinformatic Algorithms - Sequence Alignment and Suffix Trees and more Study notes Computer Science in PDF only on Docsity! CMSC423 Fall 2008 1 CMSC423: Bioinformatic Algorithms, Databases and Tools Lecture 8 Sequence alignment: exact alignment inexact alignment dynamic programming, gapped alignment CMSC423 Fall 2008 2 Suffix trees for matching • Suffix trees use O(n) space • Suffix trees can be constructed in O(n) time • Is CAT part of ATCATG ? • Match from root, char by char • If run out of query – found match • otherwise, there is no match • intuition: CAT is the prefix of some suffix AT 1,2 G$ 6,7 T 2,2 CATG$ 3,7 G$ 6,7 CATG$ 3,7 G$ 6,7 CATG$ 3,7 4 1 6 5 2 3 $ 7,7 7 CMSC423 Fall 2008 5 Why do we care? • Suffix trees are used for – mapping reads to a genome (e.g. personal genomics) – comparing genomes (comparative genomics) – finding repeats – identifying genome signatures • Exact matching – what to expect on exams – build a suffix tree for a string – answer some questions about one of the algorithms, e.g. for Z algorithm – is it necessary j be the farthest reaching Z- value or just any Z value extending past i? – do something with the help of some of the algorithms (e.g. look for repeats that occur exactly twice, etc.) CMSC423 Fall 2008 6 Suffix arrays • Suffix trees are expensive > 20 bytes / base • Suffix arrays: lexicographically sort all suffixes • Can quickly find the correct suffix through binary search • Note: much less space, but longer running time (incur a log(n) term) ATG 4 ATCATG 1 CATG 3 G 6 TCATG 2 TG 5 CMSC423 Fall 2008 7 Suffix arrays and compression • Burrows-Wheeler transform BANANA BANANA$ ANANA$B NANA$BA ANA$BAN NA$BANA A$BANAN $BANANA $BANANA A$BANAN ANA$BAN ANANA$B BANANA$ NA$BANA NANA$BA sort ANNB$AA compress character before the suffix BWT Note: characters in last column occur in same order as in first column Useful for matching within BWT