geoscience.net logo
+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

CLASS2: accurate and efficient splice variant annotation from RNA-seq reads


, : CLASS2: accurate and efficient splice variant annotation from RNA-seq reads. Nucleic Acids Research 44(10): E98-E98

Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to accurately capture splicing variation has proven difficult. Current programs can find major isoforms of a gene but miss lower abundance variants, or are sensitive but imprecise. CLASS2 is a novel open source tool for accurate genome-guided transcriptome assembly from RNA-seq reads based on the model of splice graph. An extension of our program CLASS, CLASS2 jointly optimizes read patterns and the number of supporting reads to score and prioritize transcripts, implemented in a novel, scalable and efficient dynamic programming algorithm. When compared against reference programs, CLASS2 had the best overall accuracy and could detect up to twice as many splicing events with precision similar to the best reference program. Notably, it was the only tool to produce consistently reliable transcript models for a wide range of applications and sequencing strategies, including ribosomal RNA-depleted samples. Lightweight and multi-threaded, CLASS2 requires <3GB RAM and can analyze a 350 million read set within hours, and can be widely applied to transcriptomics studies ranging from clinical RNA sequencing, to alternative splicing analyses, and to the annotation of new genomes.

US$19.90

PMID: 26975657

DOI: 10.1093/nar/gkw158


Other references

Walford, G.; Loscalzo, J., 2003: Nitric oxide in vascular biology. Nitric oxide is a highly versatile heterodiatomic molecule that effects a variety of actions in the vasculture. Originally identified as a principal determination of vascular tone, nitric oxide has since been recognized to exert anti thrombotic, a...

Boissevain, C.H., 1933: The production of tuberculous tissue and hypersensitiveness to tuberculin in guinea pigs. Exp. showed that during purification of the phosphatide from tubercle bacilli, the powers to provoke formation of tuberculous tissue and to cause hypersensitiveness to tuberculin are lost simultaneously. No conc. of material causing formation of t...

Serwotka-Suszczak, A.M.; Sochaj-Gregorczyk, A.M.; Pieczykolan, J.; Krowarsch, D.; Jelen, F.; Otlewski, J., 2017: A Conjugate Based on Anti-HER2 Diaffibody and Auristatin E Targets HER2-Positive Cancer Cells. Antibody-drug conjugates (ADCs) have recently emerged as efficient and selective cancer treatment therapeutics. Currently, alternative forms of drug carriers that can replace monoclonal antibodies are under intensive investigation. Here, a cytotox...

Gandy, Doreen G., 1967: The epidemiology of bacterial blotch of the cultivated Mushroom. Cropping was not reduced by Pseudomonas tolaasii but many fruitbodies were spoiled. The disease spread fairly slowly and incidence and severity were directly related to inoculum conc. Symptoms were more severe if the mushrooms were covered with mo...

Meeuwissen, G.; Ouwerkerk, A.; Slaterus, R., 2001: Alpine accentors in Den Helder in April 2000 and on Terschelling in May 2000 Alpenheggenmussen in Den Helder in april 2000 en op Terschelling in mei 2000. Dutch Birding, 231: 1-4

Bhat, N.; Gaensbauer, J.; Peek, R.M.; Bloch, K.; Tham, K-Toe.; Blaser, M.J.; Perez-Perez, G., 2005: Local and systemic immune and inflammatory responses to Helicobacter pylori strains. Colonization with Helicobacter pylori eventuates in varied clinical outcomes, which relate to both bacterial and host factors. Here we examine the relationships between cagA status, serum and gastric juice antibody responses, and gastric inflammat...

Janecek, Z., 1960: Functional replacement of the anal sphincter. Rozhledy V Chirurgii 39: 614-619

Weberg Erik D., 1987: Hingeward wedging in layered sequences, Sun River Canyon, Northwest Montana. Abstracts with Programs Geological Society of America: , Pages 341. 1987.

Gan, K.S.; Choo, K.T.; Lim, S.C.; Mohd Dahlan Jantan, 2001: Timber notes - medium hardwoods V (perah, petaling, punah, ranggu, rengas). This paper presents the wood characteristics, wood properties (wood density, drying properties, machining properties, durability, wood strength), and uses of perah (Elateriospermum tapos), petaling (Ochanostachys amentacea), punah (Tetramerista gl...

Monger, W.A.; Purcell, P.C.; Halford, N.G.; Acaster, M.; Thomas, T., 1995: Analyses of transgenic sugar beet hairy roots containing an antisense SNF-1-related protein kinase sequence. Journal of Experimental Botany 46(SUPPL ): 41