A memory-efficient algorithm for multiple sequence alignment with constraints

Bioinformatics
Chin Lung Lu, Yen Pin Huang

Abstract

Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficiently obtain a constrained alignment of several sequences. However, the kernels of these programs, the dynamic programming algorithms for computing an optimal constrained alignment between two sequences, run in (gamman2) memory, where gamma is the number of the constraints and n is the maximum of the lengths of sequences. As a result, such a high memory requirement limits the overall programs to align short sequences only. We adopt the divide-and-conquer approach to design a memory-efficient algorithm for computing an optimal constrained alignment between two sequences, which greatly reduces the memory requirement of the dynamic programming approaches at the expense of a small constant factor in CPU time. This new algorithm consumes only O(alphan) space, where alpha is the sum of the lengths of constraints and usually alpha < n in practical applications...Continue Reading

References

Oct 1, 1992·Computer Applications in the Biosciences : CABIOS·E Depiereux, E Feytmans
Jul 1, 1992·Bulletin of Mathematical Biology·S C ChanD K Chiu
Jan 1, 1991·Proteins·G D SchulerD J Lipman
Nov 25, 1988·Nucleic Acids Research·F Corpet
Jan 1, 1987·Journal of Molecular Evolution·D F Feng, R F Doolittle
Mar 1, 1988·Computer Applications in the Biosciences : CABIOS·E W Myers, W Miller
Jun 1, 1987·Computer Applications in the Biosciences : CABIOS·W R Taylor
Jan 1, 1993·Bulletin of Mathematical Biology·D Gusfield
Jun 12, 1996·Gene·U TöngesA W Dress
Jan 1, 1994·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·K M ChaoW Miller
Jan 1, 1994·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·W R Taylor
Jan 1, 1994·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·L Wang, T Jiang
Jan 1, 1996·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·G MyersW Miller
Feb 26, 1998·Computer Applications in the Biosciences : CABIOS·J StoyeA W Dress
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Jan 12, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M Lermen, K Reinert
Mar 26, 2002·BioTechniques·Andreas M RickertPeter J Oefner
Apr 23, 2002·Pharmacogenomics·Cédric Notredame
Oct 10, 2003·Bioinformatics·Michael SammethJens Stoye
Aug 4, 2004·Journal of Bioinformatics and Computational Biology·Chuan Yi TangWei-I Chou

❮ Previous
Next ❯

Citations

Apr 8, 2010·The Protein Journal·Zhonglong Zheng, Jie Yang
May 25, 2012·Medical & Biological Engineering & Computing·F J LopezA Blanco
Jun 10, 2009·Tissue Engineering. Part B, Reviews·Amanda W LundGeorge E Plopper
May 10, 2007·Nucleic Acids Research·Yun-Sheng ChungChin Lung Lu
May 13, 2008·Computational Biology and Chemistry·Mugdha KhaladkarJason T L Wang
May 23, 2006·Current Opinion in Structural Biology·Roland L Dunbrack
Aug 13, 2013·PLoS Genetics·Alon WellnerDan S Tawfik
Oct 24, 2014·PLoS Computational Biology·Seth D AxenCheryl A Kerfeld
Mar 8, 2013·PloS One·Marcus StammLucy R Forrest
May 15, 2013·PloS One·Christian Julian Villabona-ArenasMaurício L Nogueira
Jul 11, 2013·PloS One·Małgorzata DudkiewiczKrzysztof Pawłowski
Nov 4, 2015·PLoS Computational Biology·David BednarJiri Damborsky
Mar 20, 2014·PloS One·Ana M S GuimaraesJoanne B Messick
Nov 14, 2013·PloS One·Bas B Oude MunninkLia van der Hoek

❮ Previous
Next ❯

Software Mentioned

DC
BestScore
Clustal W
- ME ( tool for Multiple Sequence Alignment Constraints
CPSA
ME
Clustal
Linux
BestScoreRev
MuSiC

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.