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Adding unaligned sequences into an existing alignment using MAFFT and LAST

Kazutaka Katoh, Martin C. Frith
2012 Bioinformatics  
Two methods to add unaligned sequences into an existing multiple sequence alignment have been implemented as the '--add' and '--addfragments' options in the MAFFT package.  ...  These methods internally infer the phylogenetic relationship among the sequences in the existing alignment and the phylogenetic positions of unaligned sequences.  ...  They also thank Viet Huy Dinh and Shaq Liu, Osaka University, for computational support. FUNDING KAKENHI for Young Scientists (B) 21700326 from Monbukagakusho, Japan (to K.K.).  ... 
doi:10.1093/bioinformatics/bts578 pmid:23023983 pmcid:PMC3516148 fatcat:md6kpinerrgatgrzwhau42dnvu

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

K. Katoh, D. M. Standley
2013 Molecular biology and evolution  
This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing  ...  MAFFT has a subprogram, mafft-profile, to align two existing alignments. mafft-profile alignment1 alignment2 > output This method separately converts alignment1 and align-ment2 to profiles and then aligns  ...  André Lévesque, and Christopher Lewis, Agriculture and Agri-Food Canada, for permitting the use of the ITS data in this article and providing other challenging problems.  ... 
doi:10.1093/molbev/mst010 pmid:23329690 pmcid:PMC3603318 fatcat:galmrukjsbgylapsnix32vbfve

MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information

Jimin Pei, Nick V. Grishin
2006 Nucleic Acids Research  
of alignment parameters and performance tests; (iii) reference-independent evaluation of alignment quality using sequence alignmentdependent structure superpositions correlates well with reference-dependent  ...  We have developed MUMMALS, a program to construct multiple protein sequence alignment using probabilistic consistency.  ...  ACKNOWLEDGEMENTS The authors would like to thank Bong-Hyun Kim for the program to calculate reference-independent sequence and structural scores and Dr Kazutaka Katoh for providing the HOMSTRAD datasets  ... 
doi:10.1093/nar/gkl514 pmid:16936316 pmcid:PMC1636350 fatcat:uuiewf53fncvdl23d5u5aegeta

PoMSA: An Efficient and Precise Position-based Multiple Sequence Alignment Technique [article]

Sara Shehab, Sameh Shohdy, Arabi E. Keshk
2017 arXiv   pre-print
On the contrary of existing techniques, PoMSA uses position matrix instead of distance matrix to correctly adding gaps in sequences which improve the efficiency of the alignment operation.  ...  Multiple Sequence Alignment (MSA) is the main obstacle to proper design and develop homology and evolutionary modeling applications since these kinds of applications require an effective MSA technique  ...  The main goal of these algorithms is to use a clustering method to build a guide tree by adding target sequences to this tree in a sequential way that construct MSA for the given unaligned sequences [  ... 
arXiv:1708.01508v1 fatcat:mx2w5dkkabdihbsb7akghnwj7u

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh, John Rozewicki, Kazunori D. Yamada
2017 Briefings in Bioinformatics  
Multiple sequence alignment (MSA) is an important step in comparative analyses of biological sequences. We provide an online service for computing MSAs on the Web using MAFFT [1, 2] .  ...  Here, we describe usage of these functions, including recently added ones, and several tips for using our online service.  ...  If a reliable MSA and a set of unaligned sequences are given to ment/server/add_sequences.html, then an MSA of all the sequences is returned, in which the existing MSA is preserved  ... 
doi:10.1093/bib/bbx108 pmid:28968734 fatcat:hkwh5tskjbc2hith2rhnmuyrci

eMAFFTadd: scaling MAFFT-linsi-add to large datasets [article]

Chengze Shen, Baqiao Liu, Tandy Warnow
2022 bioRxiv   pre-print
and then adding the remaining sequences into the backbone alignment.  ...  There are also standalone methods, such as MAFFT--add, that can add sequences into backbone alignments, but the best version of this method (which uses --linsi) is computationally intensive.  ...  Given an existing alignment (backbone alignment) and unaligned query sequences, it adds queries to the backbone alignment using MAFFT-linsi-add with a divide-and-conquer approach inspired by UPP [14,  ... 
doi:10.1101/2022.05.23.493139 fatcat:lkwchbd4hnak7copjv3txnkyzu

Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited

Wei Wang, Ahmad Hejasebazzi, Julia Zheng, Kevin J Liu
2021 Bioinformatics  
However, the i.i.d. assumption is an over-simplification for biomolecular sequence analysis, as Felsenstein noted.  ...  Among the most widely cited and widely used such applications is the phylogenetic bootstrap method, which Felsenstein proposed in 1985 as a means to place statistical confidence intervals on an estimated  ...  Lamichhaney for help with obtaining an earlier version of the Darwin's finches dataset. We gratefully acknowledge the support of the NSF (CCF-1565719, CCF-1714417, DEB-1737898 and IOS-1740874 to K.J.  ... 
doi:10.1093/bioinformatics/btab263 pmid:34252944 fatcat:ej7pva42grfive4alctogjm5qq

Protein Multiple Sequence Alignment [chapter]

Chuong B. Do, Kazutaka Katoh
2008 Msphere  
In this chapter, we review state-of-the-art protein sequence alignment and provide practical advice for users of alignment tools.  ...  alignment tools, or in expanding the scope of tasks handled by an alignment program.  ...  C.B.D was funded by an NDSEG fellowship.  ... 
doi:10.1007/978-1-59745-398-1_25 pmid:18592193 fatcat:hjgsyxbbxrbbpe73lc73hmh53u

PASTA: Ultra-Large Multiple Sequence Alignment [chapter]

Siavash Mirarab, Nam Nguyen, Tandy Warnow
2014 Lecture Notes in Computer Science  
PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate.  ...  In this paper, we introduce a new and highly scalable algorithm, PASTA, for large-scale multiple sequence alignment estimation.  ...  MAFFT-Profile is a version of MAFFT that can add new sequences into an existing backbone alignment [22] ; we provide MAFFT-Profile the same backbone alignment that we use for the starting tree of PASTA  ... 
doi:10.1007/978-3-319-05269-4_15 fatcat:a6x35mgi3vetvm23okknn6jlgm

The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data

Seraina Klopfstein, Lars Vilhelmsen, John M. Heraty, Michael Sharkey, Fredrik Ronquist, Axel Janke
2013 PLoS ONE  
Here, we reanalyze the 18S and 28S data (unaligned about 4.4 kb) using an objective and a semi-objective alignment approach, based on MAFFT and BAli-Phy, respectively.  ...  Previous molecular analyses of higher hymenopteran relationships have largely been based on subjectively aligned ribosomal sequences (18S and 28S).  ...  Murray for part of the sequence data, and Susanne Schulmeister, the Swedish Malaise Trap Project, Norman F. Johnson, and Hege Vårdal for providing additional specimens.  ... 
doi:10.1371/journal.pone.0069344 pmid:23936325 pmcid:PMC3732274 fatcat:r66tg32lhrcbnffrweyjwp573y

A Greedy Clustering Algorithm for Multiple Sequence Alignment

Rabah Lebsir, Abdesslem Layeb, Tahi Fariza
2021 International Journal of Cognitive Informatics and Natural Intelligence  
This paper presents a novel method of clustering sequences as a preliminary step to improve the final alignment; this decomposition can be used as an optimization procedure with any MSA aligner to explore  ...  The strategy was tested using classical benchmarks like BAliBASE, Sabre, Prefab4 and Oxm, and the experimental results show that it gives good results by comparing to the other aligners.  ...  After the alignment of the two closest sequences, more sequences are added by aligning them with the existing alignment. Aligning partial alignments is also possible.  ... 
doi:10.4018/ijcini.20211001.oa41 fatcat:vjoq4mye6bde5docqer23qlgg4

Making automated multiple alignments of very large numbers of protein sequences

Fabian Sievers, David Dineen, Andreas Wilm, Desmond G. Higgins
2013 Computer applications in the biosciences : CABIOS  
We investigate the general effect on the alignment quality of an MSA when adding new sequences to an existing set of un-aligned sequences.  ...  This is partly alleviated by using iterative refinement or selectively adding sequences.  ...  The initial alignment is turned into an HMM.  ... 
doi:10.1093/bioinformatics/btt093 pmid:23428640 fatcat:p4srxcrlljhllkzs5p4ykkykaa

The accuracy of several multiple sequence alignment programs for proteins

Paulo A S Nuin, Zhouzhi Wang, Elisabeth R M Tillier
2006 BMC Bioinformatics  
We tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software Simprot which creates known alignments under realistic  ...  There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences.  ...  Acknowledgements We thank Daniel Lei for helping in the analysis, RL Charlebois for critical reading of the manuscript and Joy Abramson for Simprot support.  ... 
doi:10.1186/1471-2105-7-471 pmid:17062146 pmcid:PMC1633746 fatcat:2slzmchfdvccpko6jkxfkelvha

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

Kevin Liu, Tandy J. Warnow, Mark T. Holder, Serita M. Nelesen, Jiaye Yu, Alexandros P. Stamatakis, C. Randal Linder
2011 Systematic Biology  
Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method.  ...  First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor  ...  The authors also thank Steve Evans for helpful discussions regarding the theoretical results, as well as Ron DeBry, Laura Kubatko, and two anonymous reviewers for useful suggestions.  ... 
doi:10.1093/sysbio/syr095 pmid:22139466 fatcat:bfkw2s365jaerfw2qn25wmb42m

PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach

Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2011 BMC Bioinformatics  
It uses a set of probabilistic consistency transformations to improve the posterior base-pairing and base alignment probabilities using the information of all sequences in the alignment.  ...  Using a graph-based scheme, we greedily build up the structural alignment from sequence regions with high base-pairing and base alignment probabilities.  ...  Sankoff [4] proposed an algorithm for structural alignment of a set of unaligned RNA sequences.  ... 
doi:10.1186/1471-2105-12-s1-s38 pmid:21342569 pmcid:PMC3044294 fatcat:ld5wodttivc35a6rwye6y6iciu
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