Search · four archives
Search · four archives
18 papers · ranked by Valyu relevance
Timo Lassmann, Erik LL Sonnhammer
Background The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families for conserved motifs, phylogeny, structural properties, and to improve sensitivity in homology searching. The availability of complete genome…
Amarendran R Subramanian, Michael Kaufmann, Burkhard Morgenstern
Background DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T…
Maryam Abbasi, Luís Paquete, Francisco B. Pereira
Background 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. Choosing only one parameter setting…
Yanming Wei, Zhaoyang Huang, Pinglu Zhang, Yizheng Wang + 3 more
Multiple sequence alignment (MSA) is a fundamental problem in bioinformatics. The quality of sequence alignment significantly impacts biological sequence analysis, especially that in next-generation sequencing . MSA results are widely used in various applications, including de novo genome assembly , detection of…
Dimitrios P Lyras, Dirk Metzler
Background Obtaining an accurate sequence alignment is fundamental for consistently analyzing biological data. Although this problem may be efficiently solved when only two sequences are considered, the exact inference of the optimal alignment easily gets computationally intractable for the multiple sequence alignment…
Manish Kumar
One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple…
Ari Löytynoja, Nick Goldman
We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution. This novel method…
Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J Gibson + 1 more
'Julie D Thompson'] Background Linear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational modification, cell compartment targeting, docking sites for regulatory complex assembly and protein processing and…
P. Manikandan, D. Ramyachitra
This research work focus on the multiple sequence alignment, as developing an exact multiple sequence alignment for different protein sequences is a difficult computational task. In this research, a hybrid algorithm named Bacterial Foraging Optimization-Genetic Algorithm (BFO-GA) algorithm is aimed to improve the…
Kirill Kryukov, Naruya Saitou
Background Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or…
David J Russell, Hasan H Otu, Khalid Sayood
Background We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithms. The proposed progressive alignment algorithm uses a grammar-based distance metric to determine the order in which biological sequences are…
Bryce Kille, Advait Balaji, Fritz J. Sedlazeck, Michael Nute + 1 more
'Todd J. Treangen'] With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. By identifying nucleotides across genomes which share a common ancestor, multiple genome…
Jiannan Chao, Furong Tang, Lei Xu, Lukasz Kurgan
The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately. A number of algorithms and tools for sequence alignment have been designed…
Luisa Santus, Jose Espinosa-Carrasco, Leon Rauschning, Júlia Mir-Pedrol + 12 more
'Júlia Mir-Pedrol' 'Igor Trujnara' 'Alessio Vignoli' 'Leila Mansouri' 'Athanasios Baltzis' 'Evan W Floden' 'Paolo Di\xa0Tommaso' 'Edgar Garriga' 'Adam Gudyś' 'Sebastian Deorowicz' 'Cameron Gilchrist' 'Martin Steinegger' 'Cedric Notredame'] Title: Abstract The computational complexity of many key bioinformatics problems…
Dent Earl, Ngan Nguyen, Glenn Hickey, Robert S. Harris + 22 more
'Stephen Fitzgerald' 'Kathryn Beal' 'Igor Seledtsov' 'Vladimir Molodtsov' 'Brian J. Raney' 'Hiram Clawson' 'Jaebum Kim' 'Carsten Kemena' 'Jia-Ming Chang' 'Ionas Erb' 'Alexander Poliakov' 'Minmei Hou' 'Javier Herrero' 'William James Kent' 'Victor Solovyev' 'Aaron E. Darling' 'Jian Ma' 'Cedric Notredame' 'Michael Brudno'…
Saikat Chakrabarti, Nitin Bhardwaj, Prem A Anand, Ramanathan Sowdhamini
'Ramanathan Sowdhamini'] Background Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In…
Gordon Blackshields, Fabian Sievers, Weifeng Shi, Andreas Wilm + 1 more
'Desmond G Higgins'] Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N2 for N sequences.…
Dimitrii O. Kostenko, Eugene V. Korotkov, Cristoforo Comi, Benoit Gauthier + 2 more
'Benoit Gauthier' 'Dimitrios H. Roukos' 'Alfredo Fusco'] The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an…