Literature DB >> 24751867

Fast computation of a string duplication history under no-breakpoint-reuse.

Broňa Brejová1, Martin Kravec, Gad M Landau, Tomaš Vinař.   

Abstract

In this paper, we provide an O(n log(2) n log log n log* n) algorithm to compute a duplication history of a string under no-breakpoint-reuse condition. The motivation of this problem stems from computational biology, in particular, from analysis of complex gene clusters. The problem is also related to computing edit distance with block operations, but, in our scenario, the start of the history is not fixed, but chosen to minimize the distance measure.

Entities:  

Keywords:  duplication; dynamic text; edit distance; sequence evolution

Year:  2014        PMID： 24751867      PMCID： PMC3996574          DOI： 10.1098/rsta.2013.0133

Source DB:  PubMed          Journal:  Philos Trans A Math Phys Eng Sci        ISSN： 1364-503X            Impact factor:   4.226


  8 in total

1.  Reconstructing the duplication history of tandemly repeated genes.

Authors:  Olivier Elemento; Olivier Gascuel; Marie-Paule Lefranc
Journal:  Mol Biol Evol       Date:  2002-03       Impact factor: 16.240

2.  Reconstructing histories of complex gene clusters on a phylogeny.

Authors:  Tomás Vinar; Brona Brejová; Giltae Song; Adam Siepel
Journal:  J Comput Biol       Date:  2010-09       Impact factor: 1.479

3.  CAGE: Combinatorial Analysis of Gene-cluster Evolution.

Authors:  Giltae Song; Louxin Zhang; Tomas Vinar; Webb Miller
Journal:  J Comput Biol       Date:  2010-09       Impact factor: 1.479

4.  Duplication and inversion history of a tandemly repeated genes family.

Authors:  Mathieu Lajoie; Denis Bertrand; Nadia El-Mabrouk; Olivier Gascuel
Journal:  J Comput Biol       Date:  2007-05       Impact factor: 1.479

5.  The infinite sites model of genome evolution.

Authors:  Jian Ma; Aakrosh Ratan; Brian J Raney; Bernard B Suh; Webb Miller; David Haussler
Journal:  Proc Natl Acad Sci U S A       Date:  2008-09-11       Impact factor: 11.205

6.  Lengths of chromosomal segments conserved since divergence of man and mouse.

Authors:  J H Nadeau; B A Taylor
Journal:  Proc Natl Acad Sci U S A       Date:  1984-02       Impact factor: 11.205

7.  Evolutionary history reconstruction for Mammalian complex gene clusters.

Authors:  Yu Zhang; Giltae Song; Tomás Vinar; Eric D Green; Adam Siepel; Webb Miller
Journal:  J Comput Biol       Date:  2009-08       Impact factor: 1.479

8.  Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes.

Authors:  Crystal L Kahn; Shay Mozes; Benjamin J Raphael
Journal:  Algorithms Mol Biol       Date:  2010-01-04       Impact factor: 1.405
  8 in total
  1 in total

1.  Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.

Authors:  Cristian A Velandia-Huerto; Sarah J Berkemer; Anne Hoffmann; Nancy Retzlaff; Liliana C Romero Marroquín; Maribel Hernández-Rosales; Peter F Stadler; Clara I Bermúdez-Santana
Journal:  BMC Genomics       Date:  2016-08-11       Impact factor: 3.969
  1 in total

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