Evidence map›Paper›PMID 30778233›Full record

ArticleNature biotechnology2019

SignalP 5.0 improves signal peptide predictions using deep neural networks.

José Juan Almagro Armenteros, Konstantinos D Tsirigos, Casper Kaae Sønderby, Thomas Nordahl Petersen, Ole Winther, Søren Brunak, Gunnar von Heijne, Henrik Nielsen

Abstract read
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Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,390 papers.

0numbers the graph read from it
0cells of the map it votes in
2,390citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2,390 citing papers in PubMed.

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2,330 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

José Juan Almagro ArmenterosDepartment of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby, Denmark.
Konstantinos D TsirigosDepartment of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby, Denmark.
Casper Kaae SønderbyBioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Thomas Nordahl PetersenNational Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark.
Ole WintherBioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Søren BrunakDepartment of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby, Denmark.
Gunnar von HeijneDepartment of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
Henrik NielsenDepartment of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby, Denmark. hnielsen@bioinformatics.dtu.dk.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Signal peptides (SPs) are short amino acid sequences in the amino terminus of many newly synthesized proteins that target proteins into, or across, membranes. Bioinformatic tools can predict SPs from amino acid sequences, but most cannot distinguish between various types of signal peptides. We present a deep neural network-based approach that improves SP prediction across all domains of life and distinguishes between three types of prokaryotic SPs.

Indexed as

Neural Networks, ComputerAlgorithmsAmino Acid SequenceArchaeal ProteinsBacterial ProteinsBiotechnologyComputational BiologyEukaryotaProtein Sorting SignalsSequence Analysis, ProteinSoftwareArchaeal ProteinsBacterial ProteinsProtein Sorting Signals

Identifiers

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.