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Protocols

TargetP specifications

Information


Unique identifier OMICS_03897
Name TargetP
Interface Web user interface
Restrictions to use None
Input data A single sequence or several sequences.
Input format FASTA
Output data A prediction score for each possible outcome and a predicted localization.
Output format TXT
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes

Maintainers


  • person_outline Henrik Nielsen
  • person_outline TargetP Team
  • person_outline Olof Emanuelsson

Additional information


http://www.cbs.dtu.dk/services/doc/targetp-1.1.readme

Information


Unique identifier OMICS_03897
Name TargetP
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Version 1.1b
Stability Stable
Registration required Yes
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Henrik Nielsen
  • person_outline TargetP Team
  • person_outline Olof Emanuelsson

Additional information


http://www.cbs.dtu.dk/services/doc/targetp-1.1.readme

Publications for TargetP

TargetP citations

 (1110)
library_books

Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats

2018
PLoS One
PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] Protein domains were searched by the NCBI conserved domain searching tool [] to predict their functions and conserved motifs. To predict gene localization, TargetP [] and ChloroP [] were used based on transit peptide sequences. Transmembrane domain regions were identified using TMHMM program []. The molecular function of heme oxygenase and its molecular […]

call_split

Functional analysis of a pathogenesis related thaumatin like protein gene TaLr35PR5 from wheat induced by leaf rust fungus

2018
BMC Plant Biol
PMCID: 5935958
PMID: 29728059
DOI: 10.1186/s12870-018-1297-2
call_split See protocol

[…] m and Protscale were employed to determine the amino acids compositions, physical and chemical properties and the hydrophobicity or hydrophilicity. Psort Prediction (http://psort.hgc.jp/form.html)and TargetP (http://www.cbs.dtu.dk/services/TargetP/) were used to analyze the subcellular localization. Prediction of signal peptide was performed using SignalP 4.0(http://www.cbs.dtu.dk/services/SignalP […]

library_books

Proteomic analysis of watery saliva secreted by white backed planthopper, Sogatella furcifera

2018
PLoS One
PMCID: 5935387
PMID: 29727440
DOI: 10.1371/journal.pone.0193831

[…] performed by BlastKOALA in KEGG database (http://www.kegg.jp/). Signal peptide was determined by SignalP 4.1 Server (http://www.cbs.dtu.dk/services/SignalP/). Subcelluar localization was predicted by TargetP 1.1 Server (http://www.cbs.dtu.dk/services/TargetP/). THMHH Server v. 2.0 (http://www.cbs.dtu.dk/services/ TMHMM/) was used to predict transmembrane helices in proteins. Protein domains were d […]

library_books

The Hydrophobin Like OmSSP1 May Be an Effector in the Ericoid Mycorrhizal Symbiosis

2018
Front Plant Sci
PMCID: 5938622
PMID: 29765384
DOI: 10.3389/fpls.2018.00546

[…] fold change and a FDR corrected p < 0.05 were kept for further analysis.O. maius Small Secreted Proteins (SSPs) were identified using a custom pipeline including SignalP v4 (1), WolfPSort (2), TMHMM, TargetP (3), and PS-Scan algorithms (4) as reported in Pellegrin et al. (). To assess whether symbiosis-regulated transcripts were conserved or lineage-specific (i.e., orphan genes with no similarity […]

library_books

Common Features Between the Proteomes of Floral and Extrafloral Nectar From the Castor Plant (Ricinus Communis) and the Proteomes of Exudates From Carnivorous Plants

2018
Front Plant Sci
PMCID: 5934526
PMID: 29755492
DOI: 10.3389/fpls.2018.00549

[…] blast/) and NCBI (https://blast.ncbi.nlm.nih.gov) websites. Proteins with high identity were selected for the identification of uncharacterized proteins. The subcellular localization was predicted by TargetP (http://www.cbs.dtu.dk/services/TargetP/) (Emanuelsson et al., ) and the Top Hit Domains present in the identified proteins was evaluated by PFAM Batch sequence search (https://pfam.xfam.org/s […]

library_books

OMGene: mutual improvement of gene models through optimisation of evolutionary conservation

2018
BMC Genomics
PMCID: 5923031
PMID: 29703150
DOI: 10.1186/s12864-018-4704-z

[…] Subcellular localisation predictions for all datasets were obtained using TargetP []. For the plant dataset only, TargetP was run with the –P option to predict chloroplast targeting sequences. The localisation consistency for an orthogroup O was calculated as an entropy sco […]

Citations

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TargetP institution(s)
Stockholm Bioinformatics Center, Albanova, Stockholm University, Stockholm, Sweden; Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark; Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden.

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