Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Kenneth A WatanabeQingxi J Shen

Abstract

Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Oct 12, 2002·BMJ : British Medical Journal·Phyllida Brown
Jul 19, 2003·Science·UNKNOWN Rice Full-Length cDNA ConsortiumAyako Yasunishi
Feb 17, 2005·BMC Bioinformatics·Guy St C Slater, Ewan Birney
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Jun 3, 2009·Genes & Development·Patricia Richard, James L Manley
Apr 9, 2010·Nature Reviews. Genetics·Hadas KerenGil Ast
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
Dec 24, 2010·Genome Biology·Alicia OshlackMatthew D Young
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Nov 24, 2011·Nucleic Acids Research·David M GoodsteinDaniel S Rokhsar
Apr 19, 2012·Nature Reviews. Genetics·Mark Yandell, Daniel Ence
Jun 30, 2012·Trends in Plant Science·Naeem H SyedJohn W S Brown
Mar 14, 2013·Trends in Plant Science·Marcel C Van VerkSaskia C M Van Wees
Mar 19, 2013·PLoS Neglected Tropical Diseases·Fredy Roberto Salazar GutierrezMagally del Carmen Escobar Martínez
Apr 11, 2013·Nucleic Acids Research·Jie WuChaolin Zhang
Jul 6, 2013·Cell·Igor Ulitsky, David P Bartel
Nov 5, 2013·Nature Methods·Tamara SteijgerPaul Bertone
Nov 7, 2013·Nucleic Acids Research·Todd W HarrisPaul W Sternberg
Nov 16, 2013·Nucleic Acids Research·Susan E St PierreUNKNOWN FlyBase Consortium
Jan 1, 2014·G3 : Genes - Genomes - Genetics·Stacia R EngelJ Michael Cherry

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRP028376
SRP022162
SRR650494-5
SRR1019759

Methods Mentioned

BETA
RNA-seq
Hi-seq

Software Mentioned

OLego
MySQL
Tophat
Tiling Assembly
SQLite
Assembly
Tiling Assembly BLAST
BLAST
Cufflinks
Exonerate

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.