Genome Assembly in Bioinformatics: Lecture 15 of CMSC423 Fall 2008, Study notes of Computer Science

Download Genome Assembly in Bioinformatics: Lecture 15 of CMSC423 Fall 2008 and more Study notes Computer Science in PDF only on Docsity! CMSC423: Bioinformatic Algorithms, Databases and Tools Lecture 15 Genome assembly CMSC423 Fall 2008 2 Admin • Project questions? CMSC423 Fall 2008 5 Shotgun sequencing shearing sequencing assembly original DNA (hopefully) Overview of terms Original DNA L fragments ST sequenced ends : contig 1 contig £ — -_. +. Assembly froginents a —_——_ a AMAACTCRCCTACTTATCAACCGATCOCCCRCTACCTTCTACAGCCATCATTT AAAACLUGUCTGUTTATCAACUGA LCCCCUGULACCTIUTACAGCEATCALTE AAAACLCGUCTUCTTATCAACEGA LCCCCUGEL ACCTIUTACAGCEALCALTL contig 1 contig 2 Scaffolding CMSC423 Fall 2008 6 CMSC423 Fall 2008 7 Shortest common superstring problem Given a set of strings, Σ=(s1, ..., sn), determine the shortest string S such that every si is a sub-string of S. NP-hard approximations: 4, 3, 2.89, ... Greedy algorithm (4-approximation) phrap, TIGR Assembler, CAP ...ACAGGACTGCACAGATTGATAG ACTGCACAGATTGATAGCTGA... CMSC423 Fall 2008 10 Impact of randomness – non-uniform coverage 1 2 3 4 5 6 C ov er ag e Contig Reads Imagine raindrops on a sidewalk CMSC423 Fall 2008 11 Lander-Waterman statistics L = read length T = minimum overlap G = genome size N = number of reads c = coverage (NL / G) σ = 1 – T/L E(#islands) = Ne-cσ E(island size) = L(ecσ – 1) / c + 1 – σ contig = island with 2 or more reads See chapter 4.5 CMSC423 Fall 2008 12 All pairs alignment • Needed by the assembler • Try all pairs – must consider ~ n2 pairs • Smarter solution: only n x coverage (e.g. 8) pairs are possible – Build a table of k-mers contained in sequences (single pass through the genome) – Generate the pairs from k-mer table (single pass through k- mer table) k-mer A B C D H I F G E CMSC423 Fall 2008 15 Paths through graphs and assembly • Hamiltonian circuit: visit each node (city) exactly once, returning to the start A B D C E H G I F A B C D H I F G E Genome CMSC423 Fall 2008 16 Sequencing by hybridization AAAA AAAC AAAG AAAT AACA AACG AACT AAGA ... probes - all possible k-mers AACAGTAGCTAGATG AACA TAGC AGAT ACAG AGCT GATG CAGT GCTA AGTA CTAG GTAG TAGA CMSC423 Fall 2008 17 Assembling SBH data Main entity: oligomer (overlap) Relationship between oligomers: adjacency ACCTGATGCCAATTGCACT... CTGAT follows CCTGA (they share 4 nucleotides: CTGA) Problem: given all the k-mers, find the original string In assembly: fake the SBH experiment - break the reads into k-mers CMSC423 Fall 2008 20 deBruijn graph of Mycoplasma genitalium Read-length vs. genome complexity Bacillus anthracis Ames Bacillus subtilis Mycoplasma genitalium Mycoplasma synoviae 53 Chlamydia trachomatis A HAR-13 Haemophilus influenzas Streptococcus pneumonias TIGR4 Listeria monocytogenes OoO-w+bo $+o4 Escherichia coli K12 Yorsinia pastis COO2 CMSC423 Fall 2008 21