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Protocols

Expresso specifications

Information


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

Documentation


Publication for Expresso

Expresso citations

 (180)
library_books

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

2018
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 […]

library_books

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

2018
Neuron
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. […]

library_books

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

2018
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 […]

call_split

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

2018
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 […]

library_books

Framework for Parallel Preprocessing of Microarray Data Using Hadoop

2018
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 = […]

library_books

Signal peptides for recombinant protein secretion in bacterial expression systems

2018
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 […]

Citations

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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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