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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 in publications

 (153)
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., motor neuron soma size […]

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 […]

PMCID: 5919687
PMID: 29659563
DOI: 10.1371/journal.pcbi.1006101

[…] topology of the catalytic domain within each aars class., sequence positions of all structures in the dataset were unified using a multiple sequence alignment (msa) generated with the t-coffee expresso pipeline [] (section mapping of binding sites, and files). this type of msa is backed by the additional structural alignment of protein structures. hence, the structurally conserved […]

PMCID: 5896349
DOI: 10.1155/2018/9391635

[…]   -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 = […]

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

[…] are included within the article., not applicable., not applicable., 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 […]


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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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