TRAPID protocols

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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 in pipelines

 (4)
2017
PMCID: 5515871
PMID: 28769963
DOI: 10.3389/fpls.2017.01260

[…] assembly shows the average length is approximately 1,301 bp, n50 score of 1,953 bp, and a gc content of 0.4, among others (supplementary figure )., sequence similarity searches (rapsearch2) using trapid () revealed that significant protein hits were found for 88,454 contigs against the plaza reference proteome with top matches against vitis vinifera (8,339), oryza sativa ssp. indica (7,691), […]

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

[…] to accurately quantify expression levels reducing biases between conditions and samples (trapnell et al., ). the completeness and quality of the assembled transcriptome was assessed with busco and trapid (simão et al., ; van bel et al., ). differentially expressed transcripts between treatments were identified with cuffdiff 2.1.1 (default parameters plus—multi‐read‐correct […]

2015
PMCID: 4338194
PMID: 25706301
DOI: 10.1371/journal.pone.0118231

[…] hampering to identify protein family groups., additional functional, comparative and phylogenetic analysis of de novo transcriptome of sgb and b. mori genome was performed using the online tool trapid. of all the groups shown in , many presented gene expansion or depletion among the gene families identified. in the serine protease group, the most notorious change occurred in family […]

2015
PMCID: 4447352
PMID: 26020526
DOI: 10.1371/journal.pone.0127593

[…] scaffolds. other modified parameters included the number of scaffolds > 800 base pairs (bp) and the number of bp in scaffolds > 800 bp., assembled transcriptomes were uploaded to the program trapid [] where transcripts could be identified by protein domains related to terpene synthases (ipr005630). transcripts were then blasted on ncbi using blastx [] with the nr database for putative […]


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TRAPID in publications

 (22)
PMCID: 5751042
PMID: 29220486
DOI: 10.1093/gbe/evx259

[…] 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., to detect […]

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

[…] to plos one policies on sharing data and materials is unaltered., current address: global health economics, outcomes and epidemiology, shire international gmbh, zug, switzerland, ¶ membership of the trapid-ami investigators is provided in the acknowledgments., the 1-hour (h) algorithm triages patients presenting with suspected acute myocardial infarction (ami) to the emergency department (ed) […]

PMCID: 5737880
PMID: 28922794
DOI: 10.1093/gbe/evx160

[…] 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 […]

PMCID: 5787841
PMID: 28703416
DOI: 10.1111/pbi.12793

[…] 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 […]

PMCID: 5515871
PMID: 28769963
DOI: 10.3389/fpls.2017.01260

[…] as fragments per kilobase of transcript per million mapped reads (fpkm), was performed with edger () using the longest assigned contig as the representative transcript length for normalization., the trapid plant-specific pipeline () was adopted to assign functional annotations (e.g., gene ontology, go; plaza gene families) to the de novo assembled transcriptome with the following parameters; […]


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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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