SCAMPI protocols

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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 in pipeline

2013
PMCID: 3724490
PMID: 23663308
DOI: 10.1186/1471-2164-14-317

[…] using matgat 2.03 [] using default settings (blosum50 matrix, gap opening and extending gap penalty set to 12 and 2, respectively). transmembrane domains of t. urticae abcs were predicted using the scampi prediction server []. subcellular localization was predicted using targetp 1.0 [] . gene structures of t. urticae abcs were visualized using the coordinates of each t. urticae abc transporter […]


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SCAMPI in publications

 (17)
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 […]

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, […]

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 […]

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 […]

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 […]


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

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