Next Article in Journal
Player–Game Interaction and Cognitive Gameplay: A Taxonomic Framework for the Core Mechanic of Videogames
Previous Article in Journal
Acknowledgement to Reviewers of Informatics in 2016
Article Menu

Export Article

Open AccessArticle
Informatics 2017, 4(1), 3; doi:10.3390/informatics4010003

Alt-Splice Gene Predictor Using Multitrack-Clique Analysis: Verification of Statistical Support for Modelling in Genomes of Multicellular Eukaryotes

1
Computer Science Department, Connecticut College, 270 Mohegan Ave., New London, CT 06320, USA
2
Biology Department, Connecticut College, 270 Mohegan Ave., New London, CT 06320, USA
3
Meta Logos Inc., 124 White Birch Dr., Guilford, CT 06437, USA
4
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Antony Bryant
Received: 30 July 2016 / Revised: 25 November 2016 / Accepted: 9 January 2017 / Published: 12 January 2017
View Full-Text   |   Download PDF [5457 KB, uploaded 12 January 2017]   |  

Abstract

One of the main limitations of the typical hidden Markov model (HMM) implementation for gene structure identification is that a single structure is identified on a given sequence of genomic data—i.e., identification of overlapping structure is not directly possible, and certainly not possible within the confines of the optimal Viterbi path evaluation. This is a huge limitation given that we now know that significant portions of eukaryotic genomes, particularly mammalian genomes, are alternatively spliced, and, thus, have overlapping structure in the sense of the mRNA transcripts that result. Using the general meta-state HMM approach developed in prior work, however, more than one ‘track’ of annotation can be accommodated, thereby allowing a direct implementation of an alternative-splice gene-structure identifier. In this paper we examine the representation of alternative splicing annotation in the multi-track context, and show that the proliferation on states is manageable, and has sufficient statistical support on the genomes examined (human, mouse, worm, and fly) that a full alt-splice meta-state HMM gene finder can be implemented with sufficient statistical support. In the process of performing the alternative splicing analysis on alt-splice event counts we expected to see an increase in alternative splicing complexity as the organism becomes more complex, and this is seen with the percentage of genes with alt-splice variants increasing from worm to fly to the mammalian genomes (mouse and human). Of particular note is an increase in alternative splicing variants at the start and end of coding with the more complex organisms studied (mouse and human), indicating rapid new first and last exon recruitment that is possibly spliceosome mediated. This suggests that spliceosome-mediated refinements (acceleration) of gene structure variation and selection, with increasing levels of sophistication, has occurred in eukaryotes and in mammals especially. View Full-Text
Keywords: alternative splicing; gene-structure identification; HMM alternative splicing; gene-structure identification; HMM
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Winters-Hilt, S.; Lewis, A.J. Alt-Splice Gene Predictor Using Multitrack-Clique Analysis: Verification of Statistical Support for Modelling in Genomes of Multicellular Eukaryotes. Informatics 2017, 4, 3.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Informatics EISSN 2227-9709 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top