Cargando…

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast an...

Descripción completa

Detalles Bibliográficos
Autores principales:	Van Bel, Michiel, Proost, Sebastian, Van Neste, Christophe, Deforce, Dieter, Van de Peer, Yves, Vandepoele, Klaas
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2013
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053847/ https://www.ncbi.nlm.nih.gov/pubmed/24330842 http://dx.doi.org/10.1186/gb-2013-14-12-r134

Ejemplares similares

TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes
por: Bucchini, François, et al.
Publicado: (2021)

PLAZA 3.0: an access point for plant comparative genomics
por: Proost, Sebastian, et al.
Publicado: (2014)

De novo assembly of bacterial transcriptomes from RNA-seq data
por: Tjaden, Brian
Publicado: (2015)

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis
por: Chen, Beibei, et al.
Publicado: (2014)

Compacta: a fast contig clustering tool for de novo assembled transcriptomes
por: Razo-Mendivil, Fernando G., et al.
Publicado: (2020)

T-REx: Transcriptome analysis webserver for RNA-seq Expression data
por: de Jong, Anne, et al.
Publicado: (2015)

Comment on ‘Hayai-Annotation Plants: an ultrafast and comprehensive functional gene annotation system in plants’: the importance of taking the GO graph structure into account
por: Van Bel, Michiel, et al.
Publicado: (2020)

TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets
por: Dang, Louis T., et al.
Publicado: (2018)

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression
por: De Bodt, Stefanie, et al.
Publicado: (2009)

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets
por: Proost, Sebastian, et al.
Publicado: (2012)

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
por: Broeckx, Bart J. G., et al.
Publicado: (2015)

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
por: Ganesan, Hamilton, et al.
Publicado: (2008)

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics
por: Van Bel, Michiel, et al.
Publicado: (2018)

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines
por: Audoux, Jérôme, et al.
Publicado: (2017)

Oasis 2: improved online analysis of small RNA-seq data
por: Rahman, Raza-Ur, et al.
Publicado: (2018)

Cascade: an RNA-seq visualization tool for cancer genomics
por: Shifman, Aaron R., et al.
Publicado: (2016)

ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data
por: Romagnoli, Dario, et al.
Publicado: (2018)

Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data
por: Baerends, Richard JS, et al.
Publicado: (2004)

SeqMaT: A sequence manipulation tool for phylogenetic analysis
por: Attaluri, Pavan Kumar, et al.
Publicado: (2011)

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data
por: Gonzalez, Sergio, et al.
Publicado: (2017)

ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS
por: Romero-Losada, Ana B., et al.
Publicado: (2022)

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
por: Ambrosini, Giovanna, et al.
Publicado: (2016)

Characterizing regulatory path motifs in integrated networks using perturbational data
por: Joshi, Anagha, et al.
Publicado: (2010)

trumpet: transcriptome-guided quality assessment of m(6)A-seq data
por: Zhang, Teng, et al.
Publicado: (2018)

An online tool for obesity intervention and public health
por: Su, Jason G.
Publicado: (2016)

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics
por: Vandepoele, Klaas, et al.
Publicado: (2006)

SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies
por: Chung, Ren-Hua, et al.
Publicado: (2013)

SeqBreed: a python tool to evaluate genomic prediction in complex scenarios
por: Pérez-Enciso, Miguel, et al.
Publicado: (2020)

BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
por: Perampalam, Pirunthan, et al.
Publicado: (2020)

RiboPlotR: a visualization tool for periodic Ribo-seq reads
por: Wu, Hsin-Yen Larry, et al.
Publicado: (2021)

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
por: Fallon, Timothy R., et al.
Publicado: (2023)

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
por: Deng, Xutao
Publicado: (2011)

SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis
por: Johnson, Benjamin K., et al.
Publicado: (2016)

Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline
por: Smith, David Roy, et al.
Publicado: (2017)

An online model composition tool for system biology models
por: Coskun, Sarp A, et al.
Publicado: (2013)

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
por: Girgis, Hani Z.
Publicado: (2015)

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
por: Trinh, Quang M, et al.
Publicado: (2013)

iREAD: a tool for intron retention detection from RNA-seq data
por: Li, Hong-Dong, et al.
Publicado: (2020)

iSeqQC: a tool for expression-based quality control in RNA sequencing
por: Kumar, Gaurav, et al.
Publicado: (2020)

CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool
por: Tzfadia, Oren, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_7hth67vj2jgg46hd7dkghdhhno