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Fast computation of a string duplication history under no-breakpoint
GM, Vinař T. 2014 Fast computation of a string duplication history under no- breakpoint- reuse.Phil. Trans. R. Soc. A372: 20130133. http://dx.doi.org/10.1098/ rsta.
20130133.full.pdf

Shifted Hamming Distance: A Fast and Accurate - John Emmons
Jan 10, 2015 ... Motivation: Calculating the edit-distance (i.e., minimum number of insertions, deletions ... operations. SHD only filters string pairs that contain more errors ..... allowed error rate (Figure (a), under a fixed SRS threshold of three bps) and ..... Personalized copy number and segmental duplication maps using.
john_emmons_bioinfo2014.pdf

Shifted Hamming Distance: A Fast and Accurate SIMD-Friendly Filter
Jan 10, 2015 ... Motivation: Calculating the edit-distance (i.e., minimum number of insertions, deletions ... operations. SHD only filters string pairs that contain more errors ..... allowed error rate (Figure (a), under a fixed SRS threshold of three bps) and ..... Personalized copy number and segmental duplication maps using.
shifted-hamming-distance_bioinformatics15_proofs.pdf

Oracle® Fusion Applications Fast Formula Guide - Oracle Help Center
Sep 1, 2012 ... This software and related documentation are provided under a license ... use, duplication, disclosure, modification, and adaptation of the ... Oracle Corporation and its affiliates are not responsible for and ... Writing a Fast Formula using Expression Editor: Worked Example . ...... numeric string to a number.
e36894.pdf

Reconstructing the Duplication History of a Tandem - CiteSeerX
the history problem can not be solved by standard phy- ... Consider the two examples below in which a duplication changes .... De nition 1. A pattern is some string of nucleotides. A tandem ..... from the 2 OP T solution, cost SR is easy to compute, so we have a .... fast algorithm for the Steiner problem in graphs. Acta. Inform.
reconstructing.duplication.history.ismb.1999.pdf

Ddelta: A deduplication-inspired fast delta compression - Wen Xia
Jul 10, 2014 ... Article history: .... approach helps reduce the number of strings for delta calculation, the .... To simplify duplicate detection, Ddelta fast computes the fingerprints ..... 10 further examines the system compressing throughput under ...
DElta-PEVA-2014.pdf

Shifted Hamming distance: a fast and accurate - Bioinformatics
Feb 1, 2015 ... Motivation: Calculating the edit-distance (i.e. minimum number of ... ters string pairs that contain more errors than a user-defined threshold, making it fully com- ..... rate [(a), under a fixed SRS threshold of three bps] and variant SRS thresh- .... (2009) Personalized copy number and segmental duplication.
bioinformatics.btu856.full.pdf

Evolution of Genome Organization by Duplication and Loss - Lirmm
a specific gene family, a genome or string is a sequence of characters from. Σ where each .... alignment are the events on an evolutionary history that are not obscured by ..... computation time for the Bacillus pairs was under thirty seconds. ... fast on real datasets, such as the RNA gene repertoire of bacterial genomes.
2012-HollowayDupLossAlignment.pdf

repseek user's guide
novel functions and have been extensively studied (for a historical review see [37 ]). ... While there are some widely accepted methods to detect duplicate genes in a ... Seeds are easy to compute but unfortunately not directly suitable for most ... can be performed either at the seed level (more stringent but faster) or at the ...
Repseek_doc.pdf

Document Counting in Practice
Oct 1, 2015 ... We address the problem of counting the number of strings in a collection ... component of most ranking formulaes [22,2,3], and so fast computation of it is desirable. .... count by counting the number of values less than |P| in ILCP[sp, ep]. .... a random sequence of length m = 27 to 217, duplicating it d = 217 to.
16c000fd91d0d9fa68afede875e3a31bef17.pdf

Fast: a Transducer-Based Language for Tree Manipulation
cases it is not closed under sequential composition [22]. In the case of ... node of type HtmlE contains a tag of type string and is built using one .... Therefore, we compute the transforma- tion sani (line ..... when tree rules may delete and/or duplicate input subtrees, ..... mation about historical places and landmarks, real estate,.
pldi14.pdf

Computation and Visualization of Degenerate Repeats in Complete
Computation and Visualization of Degenerate. Repeats in .... a string, there exists a considerable number of pa- pers that ... (both tandem and non-tandem) under a general align- ment score in ..... fast database search for all k-nucleotide repeats. Nucl. .... internally repeated sequences and inferring the history of duplication.
KurOhlSchleStoGie2000.pdf

How to search in history - ScienceDirect
May 5, 2005 ... For example, we are able to give fast algorithms for locating a point in a ... S of n objects, which allows fast neighbor computation at any time in the history. ... Projects Agency under Contract N00014-83-K-0146 and ARPA Order 4786. ... This out- come is meaningless, however, if v does not belong to S(O).
1-s2.0-S0019995885800450-main.pdf?_tid=f25d8eb6-a9ea-11e3-b124-00000aab0f27&acdnat=1394631410_6f2a721858d8850348d4ce25f4378178

uthash User Guide - Troy D. Hanson
Jul 14, 2016 ... History. Your structure. The key. The hash handle. A word about memory ... It's fast as long as the hash function is suited to your keys. ..... The string is within the structure in the first example below-- name is a .... You can add the same user structure to both hash tables (without duplication of the structure), ...
userguide.pdf

The Combinatorics of Tandem Duplication Trees - Hal
Nov 26, 2007 ... any given tandem duplication history, Fitch (1977) and ... sets, this simple approach requires a fast algorithm to rec- ... of rooted and unrooted duplication trees for a number ... produce a new string σ1 ··· σn of n = m + r segments. .... The calculation of the values of p(n, k), for n = 2, ··· , 7 ... map to T under u.
D109.PDF

Optimizing Directed Acyclic Graphs via Simulated Annealing for
May 1, 2010 ... Reconstructing the evolutionary history of these ... novel fusion genes [27], genes under strong positive selection [8], ... The duplication distance, d(X, Y ), for a source string X and a .... To decide whether to accept a move or not we need to compute p ..... State Calculations by Fast Computing Machines.
hristov.pdf

Mining of Massive Datasets - Stanford InfoLab
it does not fit in main memory. Because of the ... dealing with data that arrives so fast it must be processed immediately or lost. 4. .... 2.3.7 Computing Natural Join by MapReduce . . . . . . . . . . 37 .... 3.9.2 Representing Sets as Strings . ..... 8.4.1 History of Search Advertising . ..... 11.4.5 Eliminating Duplicate Rows and Columns .
book.pdf

Optimizing data intensive GPGPU computations for - Trapnell Lab
Jun 21, 2009 ... Article history: .... Overall, MUMmerGPU 2.0 is nearly 4В faster in total computation time than the orig ... development, such as the chromosomal duplication responsible for ... does not occur in the original string р$Ю is appended to the ... suffix tree along the path of the substring matches as described below.
trapnell-schatz-optimizing-gpgpu.pdf

Introduction to Quantum Algorithms
a talk I have been giving for several years now, and discusses the history ... techniques for constructing faster algorithms for classical problems on quantum .... quantum states are invariant under multiplication by scalars, so a qubit lives in .... duplicating “gates” are not possible in the domain of quantum computing, because.
0005003

Efficient Record Linkage in Large Data Sets - The FLAMINGO
duplicate records – arises in the context of data cleansing, which is a necessary .... computing the edit distance between strings ×1 and ×2 is. З(|×1|x|×2|), where ...
dasfaa03.pdf

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