SignalP 4.0: discriminating signal peptides from transmembrane regions
By Thomas Nordahl Petersen, Søren Brunak, G. von Heijne, Henrik Nielsen. Nature Methods, 2011
8,860 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/5f704438916f83f38a2296b8315e87f629b69c63
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In Molecular Biology
- Christoph Peters
- Eugene V. Koonin
- Arne Elofsson
- David E. Gloriam
- Yuri I. Wolf
- Kira S. Makarova
- Christian Munk
- Henrik Nielsen
Citations in the corpus
- The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) (2015, methodology): “Signal peptide feature prediction employs SignalP 4.1 [20].”
- Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors (2019, methodology): “Human orphan receptor coding sequences were modified to remove predicted signal peptides (Petersen et al., 2011), methionine start codons and any internal MluI and NotI restriction sites, and were purchased from Genscript.”
- An Online Resource for GPCR Structure Determination and Analysis (2019, background): “For long N termini it is possible to replace only the signal peptide, predicted with SignalP 51 .”
- A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors (2017, positive): “Signal peptides were predicted using SignalP (Petersen et al., 2011), and transmembrane region predictions were predicted using TmHMM (Krogh et al.”
- Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression (2019, result): “Among these, we defined a consensus set of gold-standard ER-enriched genes as genes identified to be ER-associated by more than 3 of the 5 approaches (Phobius, SignalP, APEX-RIP, proximity-specific ribosome profiling, and MERFISH), resulting in a set of 590 gold-standard ER-enriched genes.”
- Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales (2015, methodology): “1c program; the union of the three predictions (gram-negative, gram-positive, and eukaryotic models) was used [45].”
- Predicting Secretory Proteins with SignalP. (2017, background): “0 from 2011 [18] is again purely ANNbased.”