FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4210367916> ?p ?o ?g. }

• W4210367916 endingPage "1440" @default.
• W4210367916 startingPage "1418" @default.
• W4210367916 abstract "Abstract Sequence mappability is an important task in genome resequencing. In the ( k , m )-mappability problem, for a given sequence T of length n , the goal is to compute a table whose i th entry is the number of indices $$j ne i$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>j</mml:mi> <mml:mo>≠</mml:mo> <mml:mi>i</mml:mi> </mml:mrow> </mml:math> such that the length- m substrings of T starting at positions i and j have at most k mismatches. Previous works on this problem focused on heuristics computing a rough approximation of the result or on the case of $$k=1$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>k</mml:mi> <mml:mo>=</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:math> . We present several efficient algorithms for the general case of the problem. Our main result is an algorithm that, for $$k=O(1)$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>k</mml:mi> <mml:mo>=</mml:mo> <mml:mi>O</mml:mi> <mml:mo>(</mml:mo> <mml:mn>1</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> , works in $$O(n)$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>O</mml:mi> <mml:mo>(</mml:mo> <mml:mi>n</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> space and, with high probability, in $$O(n cdot min {m^k,log ^k n})$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>O</mml:mi> <mml:mo>(</mml:mo> <mml:mi>n</mml:mi> <mml:mo>·</mml:mo> <mml:mo>min</mml:mo> <mml:mrow> <mml:mo>{</mml:mo> <mml:msup> <mml:mi>m</mml:mi> <mml:mi>k</mml:mi> </mml:msup> <mml:mo>,</mml:mo> <mml:msup> <mml:mo>log</mml:mo> <mml:mi>k</mml:mi> </mml:msup> <mml:mi>n</mml:mi> <mml:mo>}</mml:mo> </mml:mrow> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> time. Our algorithm requires a careful adaptation of the k -errata trees of Cole et al. [STOC 2004] to avoid multiple counting of pairs of substrings. Our technique can also be applied to solve the all-pairs Hamming distance problem introduced by Crochemore et al. [WABI 2017]. We further develop $$O(n^2)$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>O</mml:mi> <mml:mo>(</mml:mo> <mml:msup> <mml:mi>n</mml:mi> <mml:mn>2</mml:mn> </mml:msup> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> -time algorithms to compute all ( k , m )-mappability tables for a fixed m and all $$kin {0,ldots ,m}$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>k</mml:mi> <mml:mo>∈</mml:mo> <mml:mo>{</mml:mo> <mml:mn>0</mml:mn> <mml:mo>,</mml:mo> <mml:mo>…</mml:mo> <mml:mo>,</mml:mo> <mml:mi>m</mml:mi> <mml:mo>}</mml:mo> </mml:mrow> </mml:math> or a fixed k and all $$min {k,ldots ,n}$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>m</mml:mi> <mml:mo>∈</mml:mo> <mml:mo>{</mml:mo> <mml:mi>k</mml:mi> <mml:mo>,</mml:mo> <mml:mo>…</mml:mo> <mml:mo>,</mml:mo> <mml:mi>n</mml:mi> <mml:mo>}</mml:mo> </mml:mrow> </mml:math> . Finally, we show that, for $$k,m = Theta (log n)$$ <mml:math xmlns:mml=http://www.w3.org/1998/Math/MathML> <mml:mrow> <mml:mi>k</mml:mi> <mml:mo>,</mml:mo> <mml:mi>m</mml:mi> <mml:mo>=</mml:mo> <mml:mi>Θ</mml:mi> <mml:mo>(</mml:mo> <mml:mo>log</mml:mo> <mml:mi>n</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> , the ( k , m )-mappability problem cannot be solved in strongly subquadratic time unless the Strong Exponential Time Hypothesis fails. This is an improved and extended version of a paper presented at SPIRE 2018." @default.
• W4210367916 created "2022-02-08" @default.
• W4210367916 creator A5019929803 @default.
• W4210367916 creator A5051275317 @default.
• W4210367916 creator A5058155947 @default.
• W4210367916 creator A5082711976 @default.
• W4210367916 creator A5086467798 @default.
• W4210367916 creator A5090363120 @default.
• W4210367916 date "2022-02-02" @default.
• W4210367916 modified "2023-10-08" @default.
• W4210367916 title "Efficient Computation of Sequence Mappability" @default.
• W4210367916 cites W1489909987 @default.
• W4210367916 cites W1781587470 @default.
• W4210367916 cites W1963838724 @default.
• W4210367916 cites W1965815538 @default.
• W4210367916 cites W1972418517 @default.
• W4210367916 cites W1985572324 @default.
• W4210367916 cites W1995725694 @default.
• W4210367916 cites W1996780636 @default.
• W4210367916 cites W1999417916 @default.
• W4210367916 cites W2018742603 @default.
• W4210367916 cites W2024147613 @default.
• W4210367916 cites W2067974452 @default.
• W4210367916 cites W2085218027 @default.
• W4210367916 cites W2158874082 @default.
• W4210367916 cites W2165293958 @default.
• W4210367916 cites W2336925273 @default.
• W4210367916 cites W2340526756 @default.
• W4210367916 cites W2397118291 @default.
• W4210367916 cites W2747406892 @default.
• W4210367916 cites W2776892647 @default.
• W4210367916 cites W2789665539 @default.
• W4210367916 cites W2794525315 @default.
• W4210367916 cites W2885600862 @default.
• W4210367916 cites W2901938264 @default.
• W4210367916 cites W2911702276 @default.
• W4210367916 cites W2917954097 @default.
• W4210367916 cites W2946636261 @default.
• W4210367916 cites W2962720177 @default.
• W4210367916 cites W2964057579 @default.
• W4210367916 cites W3014502522 @default.
• W4210367916 cites W3104679409 @default.
• W4210367916 cites W3155786344 @default.
• W4210367916 cites W4212954813 @default.
• W4210367916 cites W4302591804 @default.
• W4210367916 doi "https://doi.org/10.1007/s00453-022-00934-y" @default.
• W4210367916 hasPublicationYear "2022" @default.
• W4210367916 type Work @default.
• W4210367916 citedByCount "0" @default.
• W4210367916 crossrefType "journal-article" @default.
• W4210367916 hasAuthorship W4210367916A5019929803 @default.
• W4210367916 hasAuthorship W4210367916A5051275317 @default.
• W4210367916 hasAuthorship W4210367916A5058155947 @default.
• W4210367916 hasAuthorship W4210367916A5082711976 @default.
• W4210367916 hasAuthorship W4210367916A5086467798 @default.
• W4210367916 hasAuthorship W4210367916A5090363120 @default.
• W4210367916 hasBestOaLocation W42103679161 @default.
• W4210367916 hasConcept C11413529 @default.
• W4210367916 hasConcept C154945302 @default.
• W4210367916 hasConcept C41008148 @default.
• W4210367916 hasConceptScore W4210367916C11413529 @default.
• W4210367916 hasConceptScore W4210367916C154945302 @default.
• W4210367916 hasConceptScore W4210367916C41008148 @default.
• W4210367916 hasFunder F4320306076 @default.
• W4210367916 hasFunder F4320306151 @default.
• W4210367916 hasFunder F4320321042 @default.
• W4210367916 hasFunder F4320322252 @default.
• W4210367916 hasFunder F4320322511 @default.
• W4210367916 hasFunder F4320335254 @default.
• W4210367916 hasIssue "5" @default.
• W4210367916 hasLocation W42103679161 @default.
• W4210367916 hasLocation W42103679162 @default.
• W4210367916 hasLocation W42103679163 @default.
• W4210367916 hasLocation W42103679164 @default.
• W4210367916 hasLocation W42103679165 @default.
• W4210367916 hasLocation W42103679166 @default.
• W4210367916 hasOpenAccess W4210367916 @default.
• W4210367916 hasPrimaryLocation W42103679161 @default.
• W4210367916 hasRelatedWork W2051487156 @default.
• W4210367916 hasRelatedWork W2073681303 @default.
• W4210367916 hasRelatedWork W2317200988 @default.
• W4210367916 hasRelatedWork W2358668433 @default.
• W4210367916 hasRelatedWork W2376932109 @default.
• W4210367916 hasRelatedWork W2382290278 @default.
• W4210367916 hasRelatedWork W2386767533 @default.
• W4210367916 hasRelatedWork W2390279801 @default.
• W4210367916 hasRelatedWork W2748952813 @default.
• W4210367916 hasRelatedWork W2899084033 @default.
• W4210367916 hasVolume "84" @default.
• W4210367916 isParatext "false" @default.
• W4210367916 isRetracted "false" @default.
• W4210367916 workType "article" @default.