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cDNA2Genome: a tool for mapping and annotating cDNAs

Coral Del Val, Karl-Heinz Glatting, Sandor Suhai
2003 BMC Bioinformatics  
for the automatic high-throughput mapping and characterization of cDNAs.  ...  and easily extensible approach to the automated mapping and annotation of human cDNAs.  ...  many useful discussions about the design of the program and during the preparation of this manuscript, and Christopher Previti for proof-reading.  ... 
doi:10.1186/1471-2105-4-39 pmid:12964951 pmcid:PMC239864 fatcat:wbhicef5q5f5zf2ivxooiu5b3i

GOPET: a tool for automated predictions of Gene Ontology terms

Arunachalam Vinayagam, Coral del Val, Falk Schubert, Roland Eils, Karl-Heinz Glatting, Sándor Suhai, Rainer König
2006 BMC Bioinformatics  
Now, this method has been made available to the public via our web-service GOPET (Gene Ontology term Prediction and Evaluation Tool). It supplies annotation for sequences of any organism.  ...  Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task.  ...  We also thank the GO consortium and all groups involved in GO annotation for making their data available through the web.  ... 
doi:10.1186/1471-2105-7-161 pmid:16549020 pmcid:PMC1434778 fatcat:5453b3cnprethipithxfg4n3su

High-throughput protein analysis integrating bioinformatics and experimental assays

C. del Val
2004 Nucleic Acids Research  
We have designed an automatic pipeline to analyse annotated open reading frames (ORFs) stemming from full-length cDNAs produced mainly by the German cDNA Consortium.  ...  The designed pipeline constitutes a new automatic approach to obtaining and administrating relevant biological data from high-throughput investigations of cDNAs in order to systematically identify and  ...  ACKNOWLEDGEMENTS We thank Dorit Arlt, Ulrike Korf and Simone Schleeger for providing information about the genomics and proteomics assays, Peter Ernst and Agnes-Hotz-Wagenblatt for many useful discussions  ... 
doi:10.1093/nar/gkh257 pmid:14762202 pmcid:PMC373366 fatcat:gpre652wsjagvlattwwdrbidkm

The Ensembl gene annotation system

Bronwen L. Aken, Sarah Ayling, Daniel Barrell, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez Banet, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier, Kevin Howe, Andreas Kähäri (+12 others)
2016 Database: The Journal of Biological Databases and Curation  
Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets.  ...  The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects.  ...  We thank the members of the Ensembl project, past and present, for their support and Guy Coates, Peter Clapham and Tim Cutts for maintaining the Ensembl computer systems. Conflict of interest.  ... 
doi:10.1093/database/baw093 pmid:27337980 pmcid:PMC4919035 fatcat:jsnympsq4rczzhh5nupzv5b4ha

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner, Seth W. Cheetham
2021 Genome Biology  
This study highlights pseudogenes as a complex and dynamic component of the human transcriptional landscape.  ...  Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes expressed in tissue-specific patterns.  ...  We aligned the reads to the human reference genome (hg38) at high stringency (q60) and compared the identified transcript isoforms to Gencode [22] annotations using SQAN TI2, a bioinformatics QC tool  ... 
doi:10.1186/s13059-021-02369-0 pmid:33971925 pmcid:PMC8108447 fatcat:plen334yhjaw5lf3u5lqjzvwee

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome [article]

Robin-Lee Troskie, Yohaann Jafrani, Tim R Mercer, Adam D Ewing, Geoffrey J Faulkner, Seth W Cheetham
2021 bioRxiv   pre-print
This study highlights pseudogenes as a complex and dynamic component of the transcriptional landscape underpinning human biology and disease.  ...  Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes.  ...  James for technical assistance, and acknowledge the Translational Research Institute (TRI) for research space and equipment that enabled this research.  ... 
doi:10.1101/2021.03.29.437610 fatcat:h3xktvbrdjgrrnoosgkgec6a4m

First 'Comprehensive' Annotation of Leucine-Rich Repeat-Containing Receptors in Rice [article]

Céline Gottin, Anne Dievart, Marilyne Summo, Gaetan Droc, Christophe Périn, Vincent Ranwez, Nathalie Chantret
2021 bioRxiv   pre-print
Using LRRprofiler, a pipeline we developed to annotate and classify those proteins, we compared three publicly available annotations of the rice Nipponbare reference genome.  ...  Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today given the urgent need for agriculture to be more sustainable.  ...  A. Cenci for critical reading of the manuscript.  ... 
doi:10.1101/2021.01.29.428842 fatcat:aat6eqoplbcevjxwktblvcpxsa

Functional Annotation of Cotesia congregata Bracovirus: Identification of Viral Genes Expressed in Parasitized Host Immune Tissues

G. Chevignon, J. Theze, S. Cambier, J. Poulain, C. Da Silva, A. Bezier, K. Musset, S. J. M. Moreau, J.-M. Drezen, E. Huguet
2014 Journal of Virology  
Gene expression was measured in triplicate on the same cDNA as that used for 454 library construction. The M. sexta rpl3 gene was used as a reference (in gray).  ...  (B) Validation of expression levels by qRT-PCR analysis of 11 selected CcBV genes on cDNA used for 454 analysis.  ...  J.T. was supported by a Ph.D. grant from the CNRS and the Région Centre.  ... 
doi:10.1128/jvi.00209-14 pmid:24872581 pmcid:PMC4136248 fatcat:olzetcnep5blzh335sopsl2wr4

Evolution of NLR resistance genes with non-canonical N-terminal domains in wild tomato species [article]

Kyungyong Seong, Eunyoung Seo, Meng Li, Brian Staskawicz
2019 bioRxiv   pre-print
Conclusions: Our study provides high quality gene models of NLRs that can serve as resources for future studies for crop engineering and elucidates greater evolutionary dynamics of the extended NLRs than  ...  Asterids and Amaranthaceae.  ...  Acknowledgements 595 We want to appreciate Freddy Monteiro for helpful discussions and guidance and Ksenia Krasileva for 596 sincere comments and advice.  ... 
doi:10.1101/786194 fatcat:yfylvzosefemlbxc2ygrg4hcyy

Work ow-based systematic design of high throughput genome annotation

Xikun Wu, Yike Guo, Fiona Tomley
Workflows were made by integrating individual bioinformatics tools into a single platform. Each workflow was designed to provide a standalone service for a particular task.  ...  In this PhD thesis, a comprehensive annotation system named as \WAGA" (Workflow-based Automatically Genome Annotation) was built and applied to the E. tenella genome.  ...  to the genome assembly 2 .3.1 ESTs mapping tools Mapping ESTs (or cDNA) sequences to genomic DNA sequences is a standard task and there are several tools for it including EST2GENOME (or EST GENOME)  ... 
doi:10.25560/6149 fatcat:r6kjzd7k5zbptls736msjvmcgu