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COFFEE: an objective function for multiple sequence alignments

C. Notredame, L. Holm, D. G. Higgins
1998 Bioinformatics  
We named it COFFEE (Consistency based Objective Function For alignmEnt Evaluation).  ...  Results: We show that multiple sequence alignments can be optimized for their COFFEE score with the genetic algorithm package SAGA.  ...  They also wish to thank the referees for their useful remarks and interesting suggestions.  ... 
doi:10.1093/bioinformatics/14.5.407 pmid:9682054 fatcat:hgetwqlljvgxron7q7bke6ivl4

An approach for COFFEE objective function to global DNA multiple sequence alignment

Anderson Rici Amorim, Leandro Alves Neves, Carlos Roberto Valêncio, Guilherme Freire Roberto, Geraldo Francisco Donegá Zafalon
2018 Computational biology and chemistry  
Nonetheless, the COFFEE objective function is not suited do perform multiple sequence alignment of nucleotides.  ...  The COFFEE objective function was implemented in the MSA-GA in order to allow it to produce better alignments to less similar sequence sets of proteins.  ...  Acknowledgment The authors would like to thank all of our collaborators and our institutions for the support to the development of the present work and São Paulo Research Foundation (FAPESP) under grant  ... 
doi:10.1016/j.compbiolchem.2018.04.012 pmid:29738913 fatcat:mter2nvglzhi5c2sclp5tw6zuq

Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks

Tuğcan KORAK, Fırat AŞIR, Esin IŞIK, Nur CENGİZ
2021 Cumhuriyet Science Journal  
Multiple sequence alignment (MSA) is a fundamental process in the studies for determination of evolutionary, structural and functional relationships of biological sequences or organisms.  ...  There are various heuristic approaches comparing more than two sequences to generate MSA. However, each tool used for MSA is not suitable for every dataset.  ...  Jens Allmer for his guidance in the conceptualization of this study. Conflicts of interest All authors declare that they have no conflict of interest.  ... 
doi:10.17776/csj.842265 fatcat:gvlsnmn5ercgfdtct6wmp4v4p4

A parallel approach of COFFEE objective function to multiple sequence alignment

G F D Zafalon, J M V Visotaky, A R Amorim, C R Valêncio, L A Neves, R C G de Souza, J M Machado
2015 Journal of Physics, Conference Series  
With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments.  ...  The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned.  ...  Thus, as an alternative, we started to use heuristic techniques, especially for multiple sequence alignment.  ... 
doi:10.1088/1742-6596/633/1/012084 fatcat:ns3okboskjhynodyc2m4i43s6i

Improvements in the sensibility of MSA-GA tool using COFFEE objective function

A R Amorim, G F D Zafalon, L A Neves, A R Pinto, C R Valêncio, J M Machado
2015 Journal of Physics, Conference Series  
The sequence alignment is one of the most important tasks in Bioinformatics, playing an important role in the sequences analysis.  ...  In this work, we have implemented the objective function COFFEE in the MSA-GA tool, in substitution of Weighted Sum-of-Pairs (WSP), to improve the final results.  ...  In this work, we proposed the implementation of COFFEE objective function in the multiple sequence alignment tool MSA-GA.  ... 
doi:10.1088/1742-6596/574/1/012104 fatcat:ctdpazmixfbsrols7fpwhp2ijq

T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton

Cédric Notredame, Desmond G Higgins, Jaap Heringa
2000 Journal of Molecular Biology  
We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacri-®ce in speed as compared to the most commonly used alternatives.  ...  With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences.  ...  Acknowledgments The authors thank the following people: Philipp Bucher for useful discussions and advice at an early stage of the project, Willie Taylor for useful discussions, Nigel Douglas for providing  ... 
doi:10.1006/jmbi.2000.4042 pmid:10964570 fatcat:53syj3ivuje6vimz7td2lkavn4

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

P. Di Tommaso, S. Moretti, I. Xenarios, M. Orobitg, A. Montanyola, J.-M. Chang, J.-F. Taly, C. Notredame
2011 Nucleic Acids Research  
This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program.  ...  This interface provides an easy and intuitive access to the most popular functionality of the package.  ...  The computational problem is the estimation of an optimal model with respect to the objective function.  ... 
doi:10.1093/nar/gkr245 pmid:21558174 pmcid:PMC3125728 fatcat:ahyqnubpkbghbipy4zs2jvekc4

Genetics of coffee quality

Thierry Leroy, Fabienne Ribeyre, Benóit Bertrand, Pierre Charmetant, Magali Dufour, Christophe Montagnon, Pierre Marraccini, David Pot
2006 Brazilian Journal of Plant Physiology  
An improvement is obtained for bean size, with significant genetic gains in current breeding programmes.  ...  Coffee quality, in the present context of overproduction worldwide, has to be considered as a main selection criterion for coffee improvement.  ...  These markers will be useful for population structure analysis and genetic mapping. Furthermore, they will allow the mapping of functional genomic sequences.  ... 
doi:10.1590/s1677-04202006000100016 fatcat:vnehnoz2tfc4hhvnfuf5awwtoa

Replacing the office intern: An autonomous coffee run with a mobile manipulator

Anthony Pratkanis, Adam Eric Leeper, Kenneth Salisbury
2013 2013 IEEE International Conference on Robotics and Automation  
This paper makes four contributions: a robust infrastructure for unifying multiple 2D navigation maps; a process for detecting and opening transparent, heavy springloaded doors; algorithms for operating  ...  We describe our development of an autonomous robotic system that safely navigates through an unmodified campus environment to purchase and deliver a cup of coffee.  ...  ACKNOWLEDGMENTS We would like to thank Guity Elahi, Victoria Quivoz, Adriana Pedroza and Leticia Cunningham of Peet's Coffee in the Clark Center for allowing the robot to enter their store and for their  ... 
doi:10.1109/icra.2013.6630731 dblp:conf/icra/PratkanisLS13 fatcat:2zrb4bh2tzeodlk4kt5dpcsi5i

Construction of coffee transcriptome networks based on gene annotation semantics

Luis F. Castillo, Narmer Galeano, Gustavo A. Isaza, Alvaro Gaitan
2012 Journal of Integrative Bioinformatics  
SummaryGene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models  ...  A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST) and Interproscan, were filtered out by coverage,  ...  Acknowledgements This work was supported by the Universidad de Caldas, the National Coffee Research Center (Cenicafé) and the Colombian Ministry of Agriculture.  ... 
doi:10.1515/jib-2012-205 fatcat:joyn6ozlyffs3nxwy2kq6angeu

Development and maintenance [chapter]

1995 From Kendal's Coffee House to Great George Street  
This paper explores the potential of low-fidelity desktop simulation as an integrated element of the overall simulation-based curriculum, and as a 'wrap-around" for high-fidelity simulation.  ...  The paper provides a series of examples to illustrate an integrated curriculum, and highlights areas in which both efficiencies and enhancements might be achieved.  ...  Not only must each curriculum component embed each of the nine events of instruction, but each component must also be aligned with an overall instructional objective and integrated into a coherent instructional  ... 
doi:10.1680/fkchtggs.20221.0003 fatcat:miocmy6wgndrjeughxolx4rz2y

Construction of coffee transcriptome networks based on gene annotation semantics

Luis F Castillo, Narmer Galeano, Gustavo A Isaza, Alvaro Gaitán
2012 Journal of Integrative Bioinformatics  
Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models.  ...  A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST) and Interproscan, were filtered out by coverage,  ...  Acknowledgements This work was supported by the Universidad de Caldas, the National Coffee Research Center (Cenicafé) and the Colombian Ministry of Agriculture.  ... 
doi:10.2390/biecoll-jib-2012-205 pmid:22829576 fatcat:2snceaevfjehhcvruasfh4x5t4

Aquaporins and the control of the water status in coffee plants

Adriana Brombini dos Santos, Paulo Mazzafera
2013 Theoretical and Experimental Plant Physiology  
Six aquaporin (AQP) homologues were identified in three coffee species (Coffea arabica, C.  ...  In order to better understand the role of these genes in coffee, C. arabica cvs Catuaí and Mundo Novo, C. canephora cv.  ...  ClustalW (Bioedit) was used to generate multiple sequence alignments.  ... 
doi:10.1590/s2197-00252013000200001 fatcat:chv5o2bzzfgfdivdyk5olyoiny

Characterization and Expression Analysis of Genes Directing Galactomannan Synthesis in Coffee

Martial Pré, Victoria Caillet, Julien Sobilo, James McCarthy
2008 Annals of Botany  
The objective of the current work was to isolate and characterize cDNA encoding proteins responsible for galactomannan synthesis in coffee and to study the expression of the corresponding transcripts in  ...  for two putative coffee mannan synthases (ManS) and two galactomannan galactosyl transferases (GMGT).  ...  We thank Valérie Chazalet, Dr Olivier Lerouxel and Dr Christelle Breton for their advice and for many helpful discussions during this work.  ... 
doi:10.1093/aob/mcn076 pmid:18562467 pmcid:PMC2712370 fatcat:qy7jolrvzja5hiwlwlsrxx2pai

Structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: a functional marker based approach [article]

Geleta Dugassa Barka, Eveline Teixeira Caixeta, Savio Siqueira Ferreira, Laercio Zambolim
2019 bioRxiv   pre-print
The characterized candidate RGA is of particular importance for further biological function analysis in coffee.  ...  For the first time, the present study has unveiled novel insights into the molecular nature of the S H genes, thereby opening new avenues for coffee rust resistance molecular breeding.  ...  RGAs were analyzed for indels and substitutions using the EMBL MUSCLE multiple174 sequence alignment tool (http://www.ebi.ac.uk/Tools/msa/muscle/) and MEGA7 [34].  ... 
doi:10.1101/763425 fatcat:cpkiud7oqvh5fc5rwxgkwrwoxq
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