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SPOCTOPUS specifications

Information


Unique identifier OMICS_03896
Name SPOCTOPUS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for SPOCTOPUS

SPOCTOPUS in pipeline

2018
PMCID: 5773712
PMID: 29348418
DOI: 10.1038/s41598-018-19491-y

[…] acid composition. multiple classifications of protein are offered in. the perception of difference between signal sequence and its peptide chain is manipulated by predictors ss- and sp-indexes. spoctopus: a combined predictor of signal peptides and membrane protein topology based on neural networks, hidden markov model (hmm) and dynamic programming algorithm is proposed in. various […]


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SPOCTOPUS in publications

 (15)
PMCID: 5773712
PMID: 29348418
DOI: 10.1038/s41598-018-19491-y

[…] acid composition. multiple classifications of protein are offered in. the perception of difference between signal sequence and its peptide chain is manipulated by predictors ss- and sp-indexes. spoctopus: a combined predictor of signal peptides and membrane protein topology based on neural networks, hidden markov model (hmm) and dynamic programming algorithm is proposed in. various […]

PMCID: 5795391
PMID: 29141914
DOI: 10.1074/mcp.RA117.000400

[…] supplemental fig. s2a) was compiled by calculating the intersections of four data sets: “predicted secreted proteins,” “signalp predicted secreted proteins,” “phobius predicted secreted proteins,” “spoctopus predicted secreted proteins” downloaded from the human protein atlas:, http://www.proteinatlas.org/search/protein_class:predicted%20secreted%20proteins, […]

PMCID: 5629013
PMID: 28945742
DOI: 10.1371/journal.pgen.1007017

[…] we constructed a rodz hybrid protein, which is fused at its c-ter to gfp and at its n-ter to the β-glucoside permease bglf, an integral membrane protein that lacks a signal sequence, as predicted by spoctopus [] and signalp 4.1 [] (which predict the sec-type signal-anchor within a protein sequences). importantly, bglf-like permeases of the phosphotransferase system (pts) were shown […]

PMCID: 5576906
PMID: 28701344
DOI: 10.1091/mbc.E15-10-0731

[…] similar sequence, such as dxφ or exy. for 8 of the candidates, the motifs reside in a region of the cargo predicted to be in the cytoplasm upon analysis using the topology prediction program spoctopus (), specifically including several dxy motifs (supplemental figure s2b and ). of note, the two validated cargoes, mep3 and ptr2, contain a dxy motif, suggesting that syp1 may promote […]

PMCID: 5145856
PMID: 28018173
DOI: 10.3389/fncel.2016.00275

[…] predicted tm topologies for or53 (topcons) were 33–53, 68–83, 123–143, 174–194, 252–272, 281–301, 354–374. for or9, six tm regions were predicted with most topcons sub-methods used. the octopus and spoctopus sub-methods, however, predicted seven tm domains at 56–76, 87–107, 148–168, 192–222, 288–308, 319–339, 389–409 with the last one being predicted only by these two algorithms., the effects […]


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SPOCTOPUS institution(s)
Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm, Sweden; Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden

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