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Space Efficient Alignment Algorithms

Space Efficient Alignment Algorithms

Space Efficient Alignment Algorithms. Dr. Nancy Warter-Perez. Outline. Algorithm complexity Complexity of dynamic programming alignment algorithms Hirschberg’s Divide and Conquer algorithm. Algorithm Complexity. Indicates the space and time (computational) efficiency of a program

By vivian
(173 views)

Digital Image Processing

Digital Image Processing

Digital Image Processing. STMIK MDP. Image Distortion Model. Restoration depends on distortion Common model: convolve plus noise Special case: noise alone (no convolution). Thoughts on Restoration. Enhancement vs restoration Enhancement: cosmetic Restoration: substantive

By mariah
(80 views)

CAP5510 – Bioinformatics Sequence Comparison

CAP5510 – Bioinformatics Sequence Comparison

CAP5510 – Bioinformatics Sequence Comparison. Tamer Kahveci CISE Department University of Florida. Goals. Understand major sequence comparison algorithms. Gain hands on experience. Why Compare Sequences ?. Prediction of function Construction of phylogeny Shotgun sequence assembly

By moshe
(160 views)

Sequence Alignment Cont’d

Sequence Alignment Cont’d

Sequence Alignment Cont’d. Sequence Alignment. AGGCTATCACCTGACCTCCAGGCCGATGCCC TAGCTATCACGACCGCGGTCGATTTGCCCGAC. - AG G CTATCAC CT GACC T C CA GG C CGA -- TGCCC --- T AG - CTATCAC -- GACC G C -- GG T CGA TT TGCCC GAC. Definition Given two strings x = x 1 x 2 ...x M , y = y 1 y 2 …y N ,

By beyla
(137 views)

Heuristic alignment algorithms; Cost matrices

Heuristic alignment algorithms; Cost matrices

Heuristic alignment algorithms; Cost matrices. 2.5 – 2.9 Thomas van Dijk. Content. Dynamic programming Improve to linear space Heuristics for database searches BLAST, FASTA Statistical significance What the scores mean Score parameters (PAM, BLOSUM). Dynamic programming.

By donar
(150 views)

L3: Blast: Keyword match basics

L3: Blast: Keyword match basics

L3: Blast: Keyword match basics. Silly Quiz. TRUE or FALSE: In New York City at any moment, there are 2 people (not bald) with exactly the same number of hairs!. Assignment 1 is online. Due 10/6 (Thursday) in class. An O(nm) algorithm for score computation. For i = 1 to n

By neviah
(133 views)

Sequence Alignment

Sequence Alignment

Sequence Alignment. Sequence Alignment. AGGCTATCACCTGACCTCCAGGCCGATGCCC TAGCTATCACGACCGCGGTCGATTTGCCCGAC. - AG G CTATCAC CT GACC T C CA GG C CGA -- TGCCC --- T AG - CTATCAC -- GACC G C -- GG T CGA TT TGCCC GAC. Definition Given two strings x = x 1 x 2 ...x M , y = y 1 y 2 …y N ,

By duane
(45 views)

Linear-Space Alignment

Linear-Space Alignment

Linear-Space Alignment. Subsequences and Substrings. Definition A string x’ is a substring of a string x, if x = ux’v for some prefix string u and suffix string v (similarly, x’ = x i …x j , for some 1  i  j  |x|) A string x’ is a subsequence of a string x

By benita
(117 views)

Linear-Space Alignment

Linear-Space Alignment

Linear-Space Alignment. Subsequences and Substrings. Definition A string x’ is a substring of a string x, if x = ux’v for some prefix string u and suffix string v (similarly, x’ = x i …x j , for some 1  i  j  |x|) A string x’ is a subsequence of a string x

By winona
(91 views)

The Complexity of Tree Transducer Output Languages

The Complexity of Tree Transducer Output Languages

The Complexity of Tree Transducer Output Languages. FSTTCS 2008, Bengaluru. The Univ. of Tokyo Kazuhiro Inaba NICTA, and UNSW Sebastian Maneth. “Complexity of Output Languages”. Given… A language L ⊆ T Σ (Trees over Σ)

By rea
(56 views)

I/O-Efficient Structures for Orthogonal Range Max and Stabbing Max Queries

I/O-Efficient Structures for Orthogonal Range Max and Stabbing Max Queries

I/O-Efficient Structures for Orthogonal Range Max and Stabbing Max Queries. Second Year Project Presentation Ke Yi Advisor: Lars Arge Committee: Pankaj K. Agarwal and Jun Yang. Problem Definition: Range Max Queries. Range-aggregate queries : range-count, range-sum, range-max

By coye
(268 views)

Sequence Alignment Cont’d

Sequence Alignment Cont’d

Sequence Alignment Cont’d. Sequence Alignment. AGGCTATCACCTGACCTCCAGGCCGATGCCC TAGCTATCACGACCGCGGTCGATTTGCCCGAC. - AG G CTATCAC CT GACC T C CA GG C CGA -- TGCCC --- T AG - CTATCAC -- GACC G C -- GG T CGA TT TGCCC GAC. Definition Given two strings x = x 1 x 2 ...x M , y = y 1 y 2 …y N ,

By rendor
(47 views)

Sequence Alignment

Sequence Alignment

Sequence Alignment. Tanya Berger-Wolf CS502: Algorithms in Computational Biology January 25, 2011. Comparing Genes in Two Genomes. Small islands of similarity corresponding to similarities between exons Such comparisons are quite common in biology research. String Similarity.

By wylie
(68 views)

A Linear Space Algorithm for Computing Maximal Common Subsequences

A Linear Space Algorithm for Computing Maximal Common Subsequences

A Linear Space Algorithm for Computing Maximal Common Subsequences. Author : D.S. Hirschberg Publisher: Communications of the ACM 1975 Presenter: Han-Chen Chen Date: 2010/04/07. Outline. Introduction Algorithm A Algorithm B Algorithm C. Introduction.

By cinnamon-mitchell
(170 views)

Presented by Daniel Khashabi

Presented by Daniel Khashabi

Pattern-independent Demosaicing ;. Presented by Daniel Khashabi Joint work with Sebastian Nowozin, Jeremy Jancsary, Andrew W. Fitzgibbon and Bruce Lindbloom. Outline. Demosaicing problem Creating input-output pairs Our demosaicing model Experiments. Raw Spcae.

By gil-cain
(214 views)

Process_Memory_Allocation

Process_Memory_Allocation

Process_Memory_Allocation. Yuan Lin 20130128. Step 1: Generate PE File (After Compile & Link ). Header. Section Table. Section .text. Section .data. Section . bss. ……. PE File Format. Step 2 : Execute PE File. 1GB. Kernel Space. Parameter & Environ. Stack. ……. Linear Space

By willoughby-roland
(65 views)

Sequence Alignment Cont’d

Sequence Alignment Cont’d

Sequence Alignment Cont’d. Evolution. Scoring Function. Sequence edits: AGGCCTC Mutations AGG A CTC Insertions AGG G CCTC Deletions AGG . CTC Scoring Function: Match: +m Mismatch: -s Gap: -d

By callum-levy
(95 views)

Sequence Alignment

Sequence Alignment

Sequence Alignment. Lecture 2, Thursday April 3, 2003. Review of Last Lecture. Lecture 2, Thursday April 3, 2003. Sequence conservation implies function. Interleukin region in human and mouse. Sequence Alignment. AGGCTATCACCTGACCTCCAGGCCGATGCCC TAGCTATCACGACCGCGGTCGATTTGCCCGAC.

By shellie-kelly
(111 views)

Linear-Space Alignment

Linear-Space Alignment

Linear-Space Alignment. Subsequences and Substrings. Definition A string x’ is a substring of a string x, if x = ux’v for some prefix string u and suffix string v (similarly, x’ = x i …x j , for some 1  i  j  |x|) A string x’ is a subsequence of a string x

By rana-hanson
(83 views)

Math 307 Spring, 2003 Hentzel Time: 1:10-2:00 MWF Room: 1324 Howe Hall

Math 307 Spring, 2003 Hentzel Time: 1:10-2:00 MWF Room: 1324 Howe Hall

Math 307 Spring, 2003 Hentzel Time: 1:10-2:00 MWF Room: 1324 Howe Hall Instructor: Irvin Roy Hentzel Office 432 Carver Phone 515-294-8141 E-mail: hentzel@iastate.edu http://www.math.iastate.edu/hentzel/class.307.ICN Text: Linear Algebra With Applications,

By india-carlson
(128 views)

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