Results 31 to 40 of about 1,513,801 (381)
Alignment Metric Accuracy [PDF]
arXiv, 2005 We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon previous approaches, and provides a balanced assessment of the fidelity of both matches and gaps.
Myers, Eugene W. +2 more
arxiv +4 more sources
Multiple sequence alignment for short sequences [PDF]
arXiv, 2015 Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of this problem, the research on this topic is focused on aligning long sequences.
arxiv +3 more sources
Heuristics for multiobjective multiple sequence alignment. [PDF]
Biomed Eng Online, 2016 Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity.
Abbasi M, Paquete L, Pereira FB.
europepmc +5 more sources
IBBOMSA: An Improved Biogeography-based Approach for Multiple Sequence Alignment [PDF]
Evolutionary Bioinformatics, 2016 In bioinformatics, multiple sequence alignment (MSA) is an NP-hard problem. Hence, nature-inspired techniques can better approximate the solution. In the current study, a novel biogeography-based optimization (NBBO) is proposed to solve an MSA problem ...
Rohit Kumar Yadav, Haider Banka
doaj +3 more sources
Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
Evolutionary Bioinformatics, 2014 A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some
Muhammad Tariq Pervez +10 more
doaj +2 more sources
Multiple sequence alignments [PDF]
Current Opinion in Structural Biology, 2005 Multiple sequence alignments are very widely used in all areas of DNA and protein sequence analysis. The main methods that are still in use are based on 'progressive alignment' and date from the mid to late 1980s. Recently, some dramatic improvements have been made to the methodology with respect either to speed and capacity to deal with large numbers ...
Desmond G. Higgins +2 more
openaire +3 more sources
EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
Algorithms for Molecular Biology, 2023 Background Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or ...
Chengze Shen +3 more
doaj +1 more source
Frontiers in Genetics, 2021 As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search.
Haipeng Shi +3 more
doaj +1 more source
The multiple alignments of very short sequences [PDF]
FASEB BioAdvances, 2021 The multiple sequence alignment (MSA) is an increasingly important task in bioinformatics as we have to deal with the constantly increasing gene- and protein sequence databases. MSA is applied in phylogenetic analysis, in discovering conservative protein domains, in the assignment of secondary and tertiary structural features in proteins, or in the ...
Kristóf Takács, Vince Grolmusz
openaire +5 more sources
Multiple alignment by sequence annealing [PDF]
Bioinformatics, 2007 AbstractMotivation: We introduce a novel approach to multiple alignment that is based on an algorithm for rapidly checking whether single matches are consistent with a partial multiple alignment. This leads to a sequence annealing algorithm, which is an incremental method for building multiple sequence alignments one match at a time.
Schwartz, Ariel S., Pachter, Lior
openaire +4 more sources