Literature DB >> 8790475

On the complexity of multiple sequence alignment.

L Wang1, T Jiang.   

Abstract

We study the computational complexity of two popular problems in multiple sequence alignment: multiple alignment with SP-score and multiple tree alignment. It is shown that the first problem is NP-complete and the second is MAX SNP-hard. The complexity of tree alignment with a given phylogeny is also considered.

Mesh：

Year:  1994        PMID： 8790475     DOI： 10.1089/cmb.1994.1.337

Source DB:  PubMed          Journal:  J Comput Biol        ISSN： 1066-5277            Impact factor:   1.479


  85 in total

1.  LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

Authors:  Michael Brudno; Chuong B Do; Gregory M Cooper; Michael F Kim; Eugene Davydov; Eric D Green; Arend Sidow; Serafim Batzoglou
Journal:  Genome Res       Date:  2003-03-12       Impact factor: 9.043

2.  A memory-efficient algorithm for multiple sequence alignment with constraints.

Authors:  Chin Lung Lu; Yen Pin Huang
Journal:  Bioinformatics       Date:  2004-09-16       Impact factor: 6.937

3.  MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Authors:  Robert C Edgar
Journal:  Nucleic Acids Res       Date:  2004-03-19       Impact factor: 16.971

4.  Comparative assessment of methods for aligning multiple genome sequences.

Authors:  Xiaoyu Chen; Martin Tompa
Journal:  Nat Biotechnol       Date:  2010-05-23       Impact factor: 54.908

5.  A novel method for multiple alignment of sequences with repeated and shuffled elements.

Authors:  Benjamin Raphael; Degui Zhi; Haixu Tang; Pavel Pevzner
Journal:  Genome Res       Date:  2004-11       Impact factor: 9.043

6.  Multiple sequence alignment by conformational space annealing.

Authors:  Keehyoung Joo; Jinwoo Lee; Ilsoo Kim; Sung Jong Lee; Jooyoung Lee
Journal:  Biophys J       Date:  2008-08-08       Impact factor: 4.033

7.  A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Authors:  Tobias Rausch; Sergey Koren; Gennady Denisov; David Weese; Anne-Katrin Emde; Andreas Döring; Knut Reinert
Journal:  Bioinformatics       Date:  2009-03-05       Impact factor: 6.937

8.  PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

Authors:  Jimin Pei; Nick V Grishin
Journal:  Methods Mol Biol       Date:  2014

Review 9.  Beyond Mfold: recent advances in RNA bioinformatics.

Authors:  Jens Reeder; Matthias Höchsmann; Marc Rehmsmeier; Björn Voss; Robert Giegerich
Journal:  J Biotechnol       Date:  2006-03-10       Impact factor: 3.307

Review 10.  Upcoming challenges for multiple sequence alignment methods in the high-throughput era.

Authors:  Carsten Kemena; Cedric Notredame
Journal:  Bioinformatics       Date:  2009-07-30       Impact factor: 6.937
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