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A Randomized Algorithm for Distance Matrix Calculations in Multiple Sequence Alignment [chapter]

Sanguthevar Rajasekaran, Vishal Thapar, Hardik Dave, Chun-Hsi Huang
2004 Lecture Notes in Computer Science  
In this paper we present a randomized algorithm to calculate distance matrices which is a major step in many multiple sequence alignment algorithms.  ...  Multiple sequence alignment (MSA) is a vital problem in biology.  ...  Although full alignment is time consuming, doing it for only a small number of sequences will give a lot better results.  ... 
doi:10.1007/978-3-540-30478-4_4 fatcat:56uwemir75clrb23qom4ggkxzy

Randomized And Parallel Algorithms For Distance Matrix Calculations In Multiple Sequence Alignment

Sanguthevar Rajasekaran, Vishal Thapar, Hardik Dave, Chun-Hsi Huang
2005 Journal of clinical monitoring and computing  
Randomized and parallel algorithms for distance matrix calculations in multiple sequence alignment. ABSTRACT. Multiple sequence alignment (MSA) is a vital problem in biology.  ...  In this paper we present a randomized algorithm to calculate distance matrices, which is a major step in many multiple sequence alignment algorithms.  ...  Our approach calculates the distance matrix for star-alignment by randomly selecting small portions of sequences and aligning them.  ... 
doi:10.1007/s10877-005-0680-3 pmid:16328949 fatcat:aoogtmm6dfhkhmevkujfo6g4n4

Distance Measures for Sequences [article]

Sandeep Hosangadi
2012 arXiv   pre-print
In this paper we compare several distance measures and examine a method that involves circular shifting one sequence against the other for finding good alignment to minimize Hamming distance.  ...  We also use run-length encoding together with LZ77 to characterize information in a binary sequence.  ...  However, the optimal string alignment algorithm calculates distance between any two sequences without using multiple edit operation.  ... 
arXiv:1208.5713v1 fatcat:ohbr5m6cv5esrgdcns5zd2jmlm

A Comparative Analysis Of Progressive Multiple Sequence Alignment Approaches Using Upgma And Neighbor Join Based Guide Trees

Dega Ravi Kumar Yadav1 And Gunes Ercal2
2018 Zenodo  
Progressive alignment involves three steps: find the distance between each pair of sequences; construct a guide tree based on the distance matrix; finally based on the guide tree align sequences using  ...  There are several ways to perform multiple sequence alignment, an important way of which is the progressive alignment approach studied in this work.  ...  ACKNOWLEDGEMENTS We would like to take this opportunity McKenney for taking their valuable  ... 
doi:10.5281/zenodo.1284963 fatcat:vw3ofwpt7rbl5c4hkso3jmlaja

Search of Fuzzy Periods in the Works of Poetry of Different Authors

Artur Nor, Eugene Korotkov
2018 Advances in Fuzzy Systems  
The technique employs genetic algorithm, dynamic programming, and the Monte Carlo method. In the present work, the technique was applied to poems written by the famous Russian and foreign classics.  ...  We applied a new method for the identification of fuzzy periods and the insertion and deletion of characters were taken into consideration while studying the works of poetry.  ...  The distance between the points is calculated as = √∑ ∑ ( 1 ( , ) − 2 ( , )) 2 (1) Here 1 ( , ) is the 1 random matrix element, and 2 ( , ) is the 2 random matrix element.  ... 
doi:10.1155/2018/4028417 fatcat:hzdvaluyhra6hjijqipugqwbny

Instability in progressive multiple sequence alignment algorithms

Kieran Boyce, Fabian Sievers, Desmond G. Higgins
2015 Algorithms for Molecular Biology  
Conclusions: This has major ramifications for both the designers of large-scale multiple sequence alignment algorithms, and for the users of these alignments.  ...  Results: We examine this tradeoff and find that, because of a loss of information in the early steps of the approach, the alignments generated by the most common multiple sequence alignment programs are  ...  Acknowledgements This work was funded by a grant from Science Foundation Ireland (11/ PI/1034). The authors thank Cedric Notredame and Maria Chatzou for useful discussions.  ... 
doi:10.1186/s13015-015-0057-1 pmid:26457114 pmcid:PMC4599319 fatcat:7cb2ibg2qjegvglynr6bh6xvlu

A Simple Genetic Algorithm for Optimizing Multiple Sequence Alignment on the Spread of the SARS Epidemic

Siti Amiroch, M. Syaiful Pradana, M. Isa Irawan, Imam Mukhlash
2019 The Open Bioinformatics Journal  
The phylogenetic tree is constructed by using the neighbor-joining algorithm with a distance matrix that the intended distance is the genetic distance obtained from sequence alignment by using the Needleman  ...  Multiple sequence alignment is a method of getting genomic relationships between 3 sequences or more.  ...  This set of distances is shown in a matrix form, named matrix of distance [5] . Example: Fig. (1) shows a distance matrix for 5 sequences, i.e.  ... 
doi:10.2174/1875036201912010030 fatcat:iza56dyygje67fsdfxulmcxrta

Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome

Eugene V. Korotkov, Yulia M. Suvorova, Dmitrii O. Kostenko, Maria A. Korotkova
2021 Genes  
A server for multiple alignment of nucleotide sequences has been created.  ...  In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.5 substitutions per position  ...  It includes pairwise comparison of N sequences, calculation of a matrix of distances between the sequences, construction of a matrix-based guide tree, and, finally, progressive MSA.  ... 
doi:10.3390/genes12020135 pmid:33494278 pmcid:PMC7909805 fatcat:v3sc6wlmv5blfikgjbpfz7nydy

Optimal Sequence Alignment and Its Relationship with Phylogeny [chapter]

Atoosa Ghahremani, Mahmood A.
2011 Bioinformatics - Trends and Methodologies  
The most common algorithm for multiple sequence alignment is BLAST.  ...  Alignment approaches Sequence alignment is a way for comparing two (pair-wise alignment) or more than two (multiple alignment) sequences.  ... 
doi:10.5772/23121 fatcat:hrtvemseyzc6jbyiyswuqcehvm

ProbPFP: a multiple sequence alignment algorithm combining hidden Markov model optimized by particle swarm optimization with partition function

Qing Zhan, Nan Wang, Shuilin Jin, Renjie Tan, Qinghua Jiang, Yadong Wang
2019 BMC Bioinformatics  
We propose a new multiple sequence alignment method combining optimized HMM and partition function in this paper.  ...  During procedures for conducting multiple sequence alignment, that is so essential to use the substitution score of pairwise alignment.  ...  Acknowledgements We thank the anonymous reviewers' valuable comments for improving the quality of this work. About this supplement  ... 
doi:10.1186/s12859-019-3132-7 pmid:31760933 pmcid:PMC6876095 fatcat:yh2sd34qzfex7mmred7whnjgxm

Twadn: an efficient alignment algorithm based on time warping for pairwise dynamic networks

Yuanke Zhong, Jing Li, Junhao He, Yiqun Gao, Jie Liu, Jingru Wang, Xuequn Shang, Jialu Hu
2020 BMC Bioinformatics  
In this paper, we proposed a novel alignment algorithm, Twadn, to align dynamic PPI networks based on a strategy of time warping.  ...  The dynamic characteristic of PPI networks is essential for understanding the evolution and regulation mechanism at the molecular level and there is still much room to improve the alignment quality in  ...  To align two sequence using DTW, we construct a matrix D m×n in which each matrix element value d ij represents distance between p i and q j i.e. d ij = 5 k=1 p ik − q jk 2 , which capture the time feature  ... 
doi:10.1186/s12859-020-03672-6 pmid:32938373 pmcid:PMC7495832 fatcat:tp4ifyisnvgjrmd4v3tuqyxyq4

OD-seq: outlier detection in multiple sequence alignments

Peter Jehl, Fabian Sievers, Desmond G. Higgins
2015 BMC Bioinformatics  
Multiple sequence alignments (MSA) are widely used in sequence analysis for a variety of tasks.  ...  The complexity of any analysis of a distance matrix is normally at least O(N 2 ) for N sequences. This is prohibitive for large N but is reduced here by using the mBed algorithm from Clustal Omega.  ...  Acknowledgements Thanks to Norma Coffey-Bargary for suggesting the interquartile range analysis. Funding was provided by Science Foundation Ireland to DGH through PI grant 11/PI/1034.  ... 
doi:10.1186/s12859-015-0702-1 pmid:26303676 pmcid:PMC4548304 fatcat:jnvljanvxbbtlpxq3obdttpb6a

Mathematical Algorithm for Identification of Eukaryotic Promoter Sequences

Eugene V. Korotkov, Yulia. M. Suvorova, Anna V. Nezhdanova, Sofia E. Gaidukova, Irina V. Yakovleva, Anastasia M. Kamionskaya, Maria A. Korotkova
2021 Symmetry  
The method for multi alignment of the promoter sequences was developed. Then, mathematical methods were developed for calculation of the statistically important classes of the promoter sequences.  ...  We developed promoter classes to search for potential promoter sequences in the rice genome with a false positive number less than 10−8 per nucleotide.  ...  As a result, the algorithm shown in Figure 2 was used to calculate the matrix a m and multiple alignment of 100 sequences for which the a m matrix was created.  ... 
doi:10.3390/sym13060917 fatcat:yjd2qvnhn5dejpx5naqw3oo2cm

TMATCH: A New Algorithm for Protein Alignments using amino-acid hydrophobicities [article]

David P Cavanaugh, Krishnan Chittur
2019 bioRxiv   pre-print
The identification of proteins of similar structure using sequence alignment is an important problem in bioinformatics.  ...  We describe TMATCH, a basic dynamic programming alignment algorithm which can rapidly identify proteins of similar structure from a database.  ...  Both calculations yield the same random match probability for any amino-acid pair comparison between the aligned search sequence and aligned comparison/match sequence.  ... 
doi:10.1101/2019.12.16.878744 fatcat:nw3ryl43drgejfn3cxezj5eati

Search for Highly Divergent Tandem Repeats in Amino Acid Sequences

Valentina Rudenko, Eugene Korotkov
2021 International Journal of Molecular Sciences  
We report a Method to Search for Highly Divergent Tandem Repeats (MSHDTR) in protein sequences which considers pairwise correlations between adjacent residues.  ...  MSHDTR was compared with some previously developed methods for searching for tandem repeats (TRs) in amino acid sequences, such as T-REKS and XSTREAM, which focus on the identification of TRs with significant  ...  Algorithmically, the phase shift is produced by a cyclic shift of the rows of the second matrix. We take the minimum of n calculated distances (B min ) as the resulting distance between two TRs.  ... 
doi:10.3390/ijms22137096 fatcat:chjtpcovsjdphemfkpxbz5kxca
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