An Almost Quadratic Time Algorithm for Sparse Spliced Alignment
The sparse spliced alignment problem consists of finding a chain of zero or more exons from O ( n ) prescribed candidate exons of a DNA sequence of length O ( n ) that is most similar to a known related gene sequence of length n . This study improves the running time of the fastest known algorithm...
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| Vydáno v: | Theory of computing systems Ročník 48; číslo 1; s. 189 - 210 |
|---|---|
| Hlavní autor: | |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
New York
Springer-Verlag
01.01.2011
Springer Nature B.V |
| Témata: | |
| ISSN: | 1432-4350, 1433-0490 |
| On-line přístup: | Získat plný text |
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| Shrnutí: | The sparse spliced alignment problem consists of finding a chain of zero or more exons from
O
(
n
) prescribed candidate exons of a DNA sequence of length
O
(
n
) that is most similar to a known related gene sequence of length
n
. This study improves the running time of the fastest known algorithm for this problem to date, which executes in
O
(
n
2.25
) time, or very recently, in
O
(
n
2
log
2
n
) time, by proposing an
O
(
n
2
log
n
)-time algorithm. |
|---|---|
| Bibliografie: | SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 |
| ISSN: | 1432-4350 1433-0490 |
| DOI: | 10.1007/s00224-009-9239-x |