Prediction of splice sites with dependency graphs and their expanded bayesian networks

Bioinformatics
Te-Ming ChenWen-Hsiung Li

Abstract

Owing to the complete sequencing of human and many other genomes, huge amounts of DNA sequence data have been accumulated. In bioinformatics, an important issue is how to predict the complete structure of genes from the genomic DNA sequence, especially the human genome. A crucial part in the gene structure prediction is to determine the precise exon-intron boundaries, i.e. the splice sites, in the coding region. We have developed a dependency graph model to fully capture the intrinsic interdependency between base positions in a splice site. The establishment of dependency between two position is based on a chi2-test from known sample data. To facilitate statistical inference, we have expanded the dependency graph (which is usually a graph with cycles that make probabilistic reasoning very difficult, if not impossible) into a Bayesian network (which is a directed acyclic graph that facilitates statistical reasoning). When compared with the existing models such as weight matrix model, weight array model, maximal dependence decomposition, Cai et al.'s tree model as well as the less-studied second-order and third-order Markov chain models, the expanded Bayesian networks from our dependency graph models perform the best in nearly al...Continue Reading

References

Jul 5, 1991·Journal of Molecular Biology·S BrunakS Knudsen
Jan 11, 1984·Nucleic Acids Research·R Staden
Oct 1, 1993·Computer Applications in the Biosciences : CABIOS·M Q Zhang, T G Marr
Apr 25, 1997·Journal of Molecular Biology·C Burge, S Karlin
Jul 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·J HendersonK H Fasman
Oct 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M G ReeseD Haussler
Mar 11, 1999·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·S SalzbergJ Henderson
Jun 8, 2000·Bioinformatics·D CaiS Kasif
Feb 27, 2001·Nucleic Acids Research·M PerteaS L Salzberg
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Sep 5, 2002·Nature Reviews. Genetics·Michael Q Zhang
Oct 5, 2002·Nucleic Acids Research·Catherine MathéPierre Rouzé
Oct 19, 2002·Bioinformatics·Masanori AritaKiyoshi Asai
Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gene Yeo, Christopher B Burge

❮ Previous
Next ❯

Citations

Jan 31, 2012·Bioinformatics·Daniel C JonesMichael G Katze
Mar 24, 2010·BMC Bioinformatics·Jens KeilwagenIvo Grosse
Jan 27, 2007·BMC Bioinformatics·A K M A BatenJason Li
Feb 27, 2008·BMC Bioinformatics·Sören SonnenburgGunnar Rätsch
Nov 19, 2008·BMC Bioinformatics·Rileen SinhaRolf Backofen
Jan 6, 2009·BMC Bioinformatics·A K M A BatenB C H Chang
Apr 6, 2006·Biology Direct·Alexander ChurbanovHesham Ali
Oct 20, 2012·Genetics and Molecular Research : GMR·J L LiZ M Yuan
Jan 26, 2016·BioData Mining·Prabina Kumar MeherAtmakuri Ramakrishna Rao
Nov 9, 2010·Computational Biology and Chemistry·Efendi Nasibov, Sezin Tunaboylu
Sep 26, 2008·Computational Biology and Chemistry·Kun-Nan TsaiChung-Ming Chen
Jan 31, 2008·Biochemical and Biophysical Research Communications·Wuritu Yang, Qian-Zhong Li
May 29, 2007·Genomics, Proteomics & Bioinformatics·T Shashi Rekha, Chanchal K Mitra
Oct 6, 2009·Journal of Biomedical Informatics·Andigoni MalousiNicos Maglaveras
Sep 10, 2014·Journal of Biomolecular Structure & Dynamics·Indrajit Mandal
Jun 16, 2016·Journal of Theoretical Biology·Prabina Kumar MeherS D Wahi
Apr 19, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Tatsuhiko Naito
Jul 23, 2020·Journal of Bioinformatics and Computational Biology·Santhosh Amilpur, Raju Bhukya

❮ Previous
Next ❯

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.