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Expresso specifications


Unique identifier OMICS_03662
Name Expresso
Interface Web user interface
Restrictions to use None
Input format FASTA
Output data The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates.
Computer skills Basic
Stability Stable
Maintained Yes


Publication for Expresso

Expresso citations


The Aerobic and Cognitive Exercise Study (ACES) for Community Dwelling Older Adults With or At Risk for Mild Cognitive Impairment (MCI): Neuropsychological, Neurobiological and Neuroimaging Outcomes of a Randomized Clinical Trial

PMCID: 5945889
PMID: 29780318
DOI: 10.3389/fnagi.2018.00076

[…] ots); or (3) game-only: the same videogame operated by a joystick or keyboard (no physical exercise was required). Exercise participants pedaled a virtual reality enhanced, recumbent stationary bike (Expresso S3R, from Interactive Fitness Holdings, LLC). Individuals in the exer-tour condition pedaled through various virtual scenic bike tours while steering along the path (but without significant c […]


Kir4.1 Dependent Astrocyte Fast Motor Neuron Interactions Are Required for Peak Strength

PMCID: 5919779
PMID: 29606582
DOI: 10.1016/j.neuron.2018.03.010

[…] regional Kir4.1 mRNA analysis, raw profiling. CEL files were obtained from the Gene Expression Omnibus website from the GEO: GSE16496 () accession ID. Expression values were generated in R using the expresso function of the affy R package with “mas” settings and no normalization. Expression values were also quantile normalized () using the SampleNetwork R function. […]


Unifying the global phylogeny and environmental distribution of ammonia oxidising archaea based on amoA genes

Nat Commun
PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] very low similarity and different length among proteins, sequences of each subunit were separately aligned with 14 different methods: L-INS-i, E-INS-i and G-INS-i strategies of MAFFT v7; PSI-Coffee, EXPRESSO; T-Coffee; ProbCons v1.12; Probalign v1.3; Prank; Muscle v3.7; MSAProbs v0.9.7; Kalign; Dialign-TX; and Clustal Omega. The 10 best alignments were selected after evaluation with MUMSA based o […]


Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

PLoS Comput Biol
PMCID: 5919687
PMID: 29659563
DOI: 10.1371/journal.pcbi.1006101
call_split See protocol

[…] ow a unified mapping of aaRS binding sites, an MSA of 81 (75) representative wild type sequences of Class I (Class II) ( and Files) aaRS was performed. The alignment was calculated with the T-Coffee expresso pipeline [], which guides the alignment by structural information. Using the obtained MSA ( and Files), residues in all aaRS structures were renumbered with the custom script “MSA PDB Renumb […]


Framework for Parallel Preprocessing of Microarray Data Using Hadoop

Adv Bioinformatics
PMCID: 5896349
DOI: 10.1155/2018/9391635

[…] fydata/”, “/home/hduser/R/data/hdfstest”)  -data<-ReadAffy()  -bgdata<-bg.correct.rma(data)  -normdata<-normalize.AffyBatch.quantiles(bgdata)   } Reducer Function   reduce <- function(){   esetExp <- expresso (normdata, bg.correct = FALSE, bgcorrect.method = NULL, normalize = FALSE, normalize.method = NULL, pmcorrect.method = “pmonly”, summary.method = “medianpolish”)  write.exprs(esetExp, file = […]


Signal peptides for recombinant protein secretion in bacterial expression systems

Microb Cell Fact
PMCID: 5875014
PMID: 29598818
DOI: 10.1186/s12934-018-0901-3

[…] Financial Support from Bio.NRW, a funding initiative of the local government of North Rhine-Westphalia is gratefully acknowledged (ExpressO, Grant-no w0805wb003c). The scientific activities of the Bioeconomy Science Center were financially supported by the Ministry of Innovation, Science and Research within the framework of the N […]


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Expresso institution(s)
Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, Marseille France; Laboratoire de systèmes périphériques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
Expresso funding source(s)
This project was supported by CNRS (Centre National de la Recherche Scientifique), Sanofi-Aventis Pharma SA., Marseille–Nice Genopole and the French National Genomic Network (RNG).

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