ArticleBMC bioinformatics2009
A comprehensive assessment of N-terminal signal peptides prediction methods.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it, 70 citations in OpenAlex.
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- The luminescent HiBiT peptide enables selective quantitation of G protein-coupled receptor ligand engagement and internalization in living cells.The Journal of biological chemistry · 2020Article
- Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences.Frontiers in genetics · 2020Review
- SEC-Translocon Dependent Extracytoplasmic Proteins ofFrontiers in microbiology · 2016Article
- Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display.Frontiers in microbiology · 2016Review
- Analysis of the Secretome of Apoptotic Peripheral Blood Mononuclear Cells: Impact of Released Proteins and Exosomes for Tissue Regeneration.Scientific reports · 2015Article
- Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors.Frontiers in plant science · 2015Article
- The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms.BMC genomics · 2013Article
- A plasmodesmal glycosyltransferase-like protein.PloS one · 2013Article
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- Secretory signal peptide modification for optimized antibody-fragment expression-secretion in Leishmania tarentolae.Microbial cell factories · 2012Article
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- Signatures of positive selection in Toll-like receptor (TLR) genes in mammals.BMC evolutionary biology · 2011Article
- SignalP 4.0: discriminating signal peptides from transmembrane regions.Nature methods · 2011Article
- Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium.BMC genomics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAmino-terminal signal peptides (SPs) are short regions that guide the targeting of secretory proteins to the correct subcellular compartments in the cell. They are cleaved off upon the passenger protein reaching its destination. The explosive growth in sequencing technologies has led to the deposition of vast numbers of protein sequences necessitating rapid functional annotation techniques, with subcellular localization being a key feature. Of the myriad software prediction tools developed to automate the task of assigning the SP cleavage site of these new sequences, we review here, the performance and reliability of commonly used SP prediction tools.
resultsThe available signal peptide data has been manually curated and organized into three datasets representing eukaryotes, Gram-positive and Gram-negative bacteria. These datasets are used to evaluate thirteen prediction tools that are publicly available. SignalP (both the HMM and ANN versions) maintains consistency and achieves the best overall accuracy in all three benchmarking experiments, ranging from 0.872 to 0.914 although other prediction tools are narrowing the performance gap.
conclusionThe majority of the tools evaluated in this study encounter no difficulty in discriminating between secretory and non-secretory proteins. The challenge clearly remains with pinpointing the correct SP cleavage site. The composite scoring schemes employed by SignalP may help to explain its accuracy. Prediction task is divided into a number of separate steps, thus allowing each score to tackle a particular aspect of the prediction.
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