TRAPID statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TRAPID
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Tool usage distribution map

This map represents all the scientific publications referring to TRAPID per scientific context
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Protocols

TRAPID specifications

Information


Unique identifier OMICS_12125
Name TRAPID
Interface Web user interface
Restrictions to use None
Input data RAPID supports properly formatted multi-fasta files, with the '>' symbol indicating the transcript identifier of the following sequence. In case the headers of the multi-fasta file consist of multiple sections separated by the '|' symbol, the first section will be used as unique identifier.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Michiel Van Bel

Publication for TRAPID

TRAPID citations

 (26)
library_books

Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant

2017
Genome Biol Evol
PMCID: 5751042
PMID: 29220486
DOI: 10.1093/gbe/evx259

[…] nalysis of RTL using Perl scripts developed by the Systems Biology Research and Resources group at Harvard University. Tentative orthologous pairs (TOPs) between CAA1 and CAB1 were analyzed using the TRAPID pipeline () to identify the longest ORF for each transcript. RBH was also used to identify the best putative ortholog for each TOP in the Arabidopsis thaliana TAIR10 CDS database. […]

library_books

Economic evaluation of the one hour rule out and rule in algorithm for acute myocardial infarction using the high sensitivity cardiac troponin T assay in the emergency department

2017
PLoS One
PMCID: 5679593
PMID: 29121105
DOI: 10.1371/journal.pone.0187662

[…] ervation zone (assumed to be same as SoC). The primary drivers for the LoS for rule-in and rule-out were the time to second blood draw and the time between the second blood draw and ED discharge. The TRAPID-AMI study observed that the time to second blood draw was around 1.7 hours with no marked site-specific variability. However, the time between the second blood draw and ED discharge was depende […]

call_split

Genome Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer)

2017
Genome Biol Evol
PMCID: 5737880
PMID: 28922794
DOI: 10.1093/gbe/evx160
call_split See protocol

[…] SRR2952867) using Trinity (). To examine the quality of assembled transcripts, we predicted the open read frame (ORF) for all transcripts and translated them into protein sequences using the program TRAPID (http://bioinformatics.psb.ugent.be/webtools/trapid). To further eliminate the data bias caused by low quality transcripts, only the transcripts that are more than 300 amino acids in length wer […]

library_books

ABA signalling manipulation suppresses senescence of a leafy vegetable stored at room temperature

2017
Plant Biotechnol J
PMCID: 5787841
PMID: 28703416
DOI: 10.1111/pbi.12793

[…] ly due to the intrinsic limitations of this benchmark with species with complex polyploidy (Simão et al., ) and the senescent nature of the material, representing very specific tissue and conditions. TRAPID (Van Bel et al., ) provided an assessment of transcripts structure and completeness, by comparing transcript length to the lengths of its associated gene family. With an average sequence length […]

library_books

Tissue Specific Floral Transcriptome Analysis of the Sexually Deceptive Orchid Chiloglottis trapeziformis Provides Insights into the Biosynthesis and Regulation of Its Unique UV B Dependent Floral Volatile, Chiloglottone 1

2017
Front Plant Sci
PMCID: 5515871
PMID: 28769963
DOI: 10.3389/fpls.2017.01260

[…] orghum) were also highly represented (Supplementary Figure ). This similarity distribution has also been reported for other orchid transcriptomes such as Phalaenopsis sp. (; ). In this study, we used TRAPID and Mercator, two widely adopted plant-specific annotation modules that has been specifically tuned to provide a good balance between sensitivity and specificity when annotating plant sequences […]

library_books

EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high throughput transcriptome data

2017
PMCID: 5737374
PMID: 28338930
DOI: 10.1093/dnares/dsx009

[…] ols. After transcripts have been assembled, the annotation is critical to define their potential function. Several tools could be applied for annotation, such as Blast2GO, BLAST, Trinotate, MAPLE and TRAPID. As well as, many database can be utilized to annotate the transcripts with regard to NCBI non-redundancy proteins (NCBI NR), UniProt Swiss-Prot/TrEMBL, Gene Ontology (GO) and KEGG pathways. Fo […]


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TRAPID institution(s)
Department of Plant Systems Biology, VIB-Universiteit Gent, Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium; University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany; Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Department of Pharmaceutics, Ghent University, Gent, Belgium; Department of Genetics, Genome Research Institute, University of Pretoria, Pretoria, South Africa

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