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Sequencing, Sequence Alignment & Software Lushan Wang, Shandong University

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A: To sequence a DNA molecule is to obtain the string of bases that it contains. ... assembly: detect 'tangles' indicative of repeats (Pevzner, Tang, Waterman 2001) ...

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... piece of sequence you want to copy. Insert the sequence into a ... The cDNA sequence represents what is expressed in a particular cell at a particular time ...

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Sequencing and Sequence Alignment CIS 667 Bioinformatics Spring 2004 Protein Sequencing Before DNA sequencing, protein sequencing was common Sanger won a Nobel prize ...

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Title: Traveling Salesman Problem and Multiple Sequence Alignment Author: weiwei Last modified by: rwr Created Date: 1/22/2003 9:38:06 PM Document presentation format

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cs570 Artificial Intelligence Chapter 3 Solving Problems By Searching and Constraint Satisfaction Problem 2000. 3. 20. Overview Solving Problem by ...

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Title: Assembling Sequences using additional information Author: Pre-installed Last modified by: Pre-installed Created Date: 9/16/1999 2:41:41 PM Document ...

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Given certain markers (small but precisely defined sequences) physical map ... Cloning ... Goal: produce large quantities of a DNA molecule without cloning. ...

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Its structure corresponds to the structure of problem solving in two important ways: ... Suppose we are trying to prove a math theorem.We can prove a lemma. ...

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the basic elements of a problem definition. initial state. operator (or successor function S) ... On holiday in Romania: currently in Arad. Flight leaves ...

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GLOBAL PAIRWISE ALIGNMENT GLOBAL ALIGNMENT OF: 2 NUCLEOTIDE SEQUENCES OR 2 AMINO-ACID SEQUENCES * To derive a mutational probability matrix for a protein sequence ...

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A heuristic for a real-life car sequencing problem with multiple requirements Daniel Aloise 1 Thiago Noronha 1 Celso Ribeiro 1,2 Caroline Rocha 2 Sebasti n Urrutia 1

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Minimize the number of paint color changes ... Initial solutions for problem RAF-EP-(ENP) will have the minimum number of paint color changes. ...

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... minimizing sequence tends to an infinitely-fast-oscillating limit. UConn, April ... There are infinitely many local minima; each corresponds to an equilibrium. ...

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Enabling Large Scale Scientific Computations for Expressed Sequence Tag Sequencing over Grid and Cloud Computing Clusters Sangmi Lee Pallickara, Marlon Pierce ...

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Therefore, there is a requirement to group vehicles together by paint color. Problem statement ... Minimize the number of paint color changes ...

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CrossWA: A new approach of combining pairwise and three-sequence alignments to improve the accuracy for highly divergent sequence alignment Che-Lun Hung, Chun-Yuan ...

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Arc-annotated sequence usage. The secondary and tertiary structure of RNA ... Alas, I know little about dynamic programming -but I know divide-and- conquer ...

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Predict protein structure using amino acid interaction preferences. Result ... Interactions between amino acids from the sequence are admitted into the score function ...

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... Symbolic Sequences for String-Matching, Pattern-Recognition and Grammar Detection ... to make fast non-exact string matching and pattern recognition. ...

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CrossWA: A new approach of combining pairwise and three-sequence alignments to improve the accuracy for highly divergent sequence alignment Che-Lun Hung, Chun-Yuan ...

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Bioinformatics. Genome Sequencing. Research Problem. Fuzzy Logic. Ongoing ... Bioinformatics ... important first step in many bioinformatics applications ...

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Objectives: At the end of the study, the student must be able to: define arithmetic sequence; know if a sequence is an arithmetic progression; apply arithmetic ...

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Arithmetic Sequence: ... Multiplier Pod Problem Week Sales 0 1 2 3 4 n 100 115 132.25 152.09 174.9 = 100.1.15.1.15 = 100.1.15 = 100.1.15.1.15.1.15 = 100.1.15.1 ...

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Be aware of the importance of sequence searching and sequence alignment in biology and medicine ... every 20 residues the alignment is suspicious. 29. Lecture ...

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Solving problems by searching Chapter 3 in AIMA Problem Solving Rational agents need to perform sequences of actions in order to achieve goals.

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SEQUENCES. SORTING. Sorting. Input: (unsorted) sequence of n elements a1, a2, ..., an ... What if you had 10,000 unsorted records and each record had a value between ...

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Most genome will be sequenced and can be sequenced; few problem are unsolvable. ... Assembly: Process of taking raw single-pass reads into ...

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3-6 Arithmetic Sequences Warm Up Problem of the Day Lesson Presentation Course 3

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Sequence Alignment

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Decoding: given a model and an output sequence, what is the most likely state sequence through the model that generated the output? A solution to this problem gives ...

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sequence alignment aggctatcacctgacctccaggccgatgccc tagctatcacgaccgcggtcgatttgcccgac-aggctatcacctgacctccaggccga--tgccc---tag-ctatcac--gaccgc--ggtcgatttgcccgac

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Sequence Alignment

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Algorithms Problem Solving

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Order Picking: Pick Sequencing and Batching The Pick Sequencing Problem Given a picking list, sequence the visits to the picking locations so that the overall ...

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Sequence Listings Sue Wolski ... Where the SL Text File is a Search Tool ... available Open in a text editor that produces files only in ASCII format Such as ...

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Large number of sequences to search your query sequence against. ... Blast of human beta globin protein against zebra fish. Sample BLAST output (cont'd) ...

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Assess ancestry among homologs (sequences with common ancestory) to help in gene ... AA--GATA ... AA--GATA. Alignment scores would be -3, -1, 1, respectively; ...

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We can think of these sequences as strings of letters. DNA & RNA: alphabet of 4 letters ... Lemma: T(m,n) 2cmn. Time complexity is linear in size of the problem ...

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Exploit the fact that similar sequences are usually evolutionarily related ... Works well for similar sequences; poorly for divergent. Problems with progressive ...

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Sequence Alignment

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Pairwise Sequence Alignment *

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DNA Sequencing DNA sequencing How we obtain the sequence of nucleotides of a species Which representative of the species? Which human? Answer one: Answer two: it ...

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Geometric Sequences (day 3) Geometric Sequence Objective: To find a formula for the nth term of a geometric sequence & To find specified terms of ...

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Start at primer (restriction site) Grow DNA chain ... ARD, CRB ? A. R. B. CS262 Lecture 9, Win06, Batzoglou. Sequencing and Fragment Assembly ...

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Pairwise Sequence Comparison Stat 246, Spring 2002, Week 5,

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Large number of sequences to search your query sequence against. ... Jukes-Cantor model. Transitions vs transversions. Kimura's 2-parameter model ...

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Leonhard Euler, 1735. Formalization of K nigsberg Bridge Problem: Graph & Eulerian Cycle ... Euler Theorem ... Euler Theorem: Proof. Eulerian balanced ...

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Evidence: mtDNA. Multiregional Evolution ... Proponents of the theory doubt mtDNA and other genetic evidence. DNA Sequencing. Goal: ...

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Stat 246, Lecture 3 Biological sequence analysis The objects of our study DNA, RNA and proteins: macromolecules which are unbranched polymers built up from smaller units.

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Biological sequence analysis Terry Speed Wald Lecture II, August 8, 2001

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Multiple Sequence Alignment An alignment of heads Sequence Alignment A way of arranging the primary sequences of DNA, RNA and amino acid to identify the regions of ...

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Costas S. Iliopoulos. Ely Porat. 2. Weighted Sequences ... Problem Definition: Given a threshold probability , find all occurrences of the ...

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Sequence motifs An (unsupervised) machine learning approach to motif discovery. Input: Set of unaligned sequences. Possible width of motifs.

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Convex Hull Problem Presented By Erion Lin Outline Convex Hull Problem Voronoi Diagram Fermat Point Outline Convex Hull Problem Voronoi Diagram Fermat Point Convex ...

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The Destination Sequenced Distance Vector (DSDV) protocol Dr. R. B. Patel The Routing Problem The property of ad-hoc networks Topology may be quite dynamic No ...

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