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SCAMPI specifications

Information


Unique identifier OMICS_07186
Name SCAMPI
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for SCAMPI

SCAMPI citations

 (17)
library_books

Early Cold Induced Peroxidases and Aquaporins Are Associated With High Cold Tolerance in Dajiao (Musa spp. ‘Dajiao’)

2018
PMCID: 5852111
PMID: 29568304
DOI: 10.3389/fpls.2018.00282

[…] website: http://banana-genome-hub.southgreen.fr/download. proteins were identified by searches using the transmembrane structure prediction software tools tmhmm server v. 2.0 (), phobius (), and scampi-single () according to the methods of . only candidate proteins that were predicted by two out of the three software programs were deemed to be mps. the change in relative concentration […]

library_books

Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans

2017
PMCID: 5620054
PMID: 28959054
DOI: 10.1038/s41598-017-11543-z

[…] multiple methods and uses a hidden-markov model to estimate the consensus topology from the methods for a predicted transmembrane protein. as recommended by the authors, the four methods used were: scampi-single; s-tmhmm; hmmtop; and memsat. to ensure that all predicted membrane proteins were valid proteins with acceptable transcriptional support and recognized protein-coding annotation, […]

library_books

High GC content causes orphan proteins to be intrinsically disordered

2017
PMCID: 5389847
PMID: 28355220
DOI: 10.1371/journal.pcbi.1005375

[…] are found in the supplementary material ( to figs). it is worth mentioning that these predictors operate with different definitions of disorder, so a consensus should not be expected., we used scampi [] to predict the fraction of transmembrane residues in a protein. the fraction of low-complexity residues is predicted using seg []. psipred [] was used to predict the secondary structure […]

library_books

Genome wide in silico identification of membrane bound transcription factors in plant species

2017
PMCID: 5694209
PMID: 29158982
DOI: 10.7717/peerj.4051

[…] were used to perform in silico analysis of membrane-bound proteins via the following bioinformatics tools., seven prediction methods including tmhmm 2.0 (), s-tmhmm (), hmmtop (), phobius (), scampi-single (), memsat 1.0 () and toppred () were chosen for tm prediction. for tmhmm 2.0, transmembrane helices and the locations were predicted; the most likely locations of transmembrane motifs […]

library_books

Topology based identification and comprehensive classification of four transmembrane helix containing proteins (4TMs) in the human genome

2016
PMCID: 4815072
PMID: 27030248
DOI: 10.1186/s12864-016-2592-7

[…] and is to use several prediction methods and make a consensus or majority decision regarding topology. topcons-single uses a consensus decision method that comprises five different prediction tools: scampi-single []; s-tmhmm []; memsat 1.0 []; hmmtop []; and phobius []. the benchmark of membrane helix predictions from sequence website was used to assess the accuracy of the methods used […]

library_books

Genome of the facultative scuticociliatosis pathogen Pseudocohnilembus persalinus provides insight into its virulence through horizontal gene transfer

2015
PMCID: 4614350
PMID: 26486372
DOI: 10.1038/srep15470

[…] to assign the protease classes. to annotate the membrane transporters, all the genes were blast searched against the tcdb transporters database, and the transmembrane helices were predicted using scampi, toppred and tmhmm. a gene was regarded as a membrane transporter if it had a blast hit in the tcdb transporters database with an e-value less than 1e-03 and showed at least one transmembrane […]


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SCAMPI institution(s)
Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden

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