Detection and prediction of alternative splicing in Arabidopsis thaliana

Int J Comput Biol Drug Des. 2008;1(1):39-58. doi: 10.1504/ijcbdd.2008.018709.

Abstract

Alternative splicing is an important process for increasing the diversity arising from a single gene. Presently, most studies aimed at detecting alternatively spliced genes use Expressed Sequence Tags (ESTs). However, the EST studies based on spliced transcripts analyse sequences by alignment rather than sequence patterns. Second, EST libraries can be of uncertain quality. To address these issues and to improve the quality of detection and prediction for alternative splicing, we propose a method that primarily uses pre-mRNAs. It is achieved by a decision tree algorithm using triplet nucleotides as attributes for each chromosome in Arabidopsis thaliana. In addition, we propose a novel algorithm for accurate prediction.

Publication types

  • Evaluation Study

MeSH terms

  • Algorithms
  • Alternative Splicing*
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Base Sequence
  • Computational Biology
  • Computer Simulation
  • Consensus Sequence
  • Conserved Sequence
  • Databases, Nucleic Acid
  • Decision Trees
  • Expressed Sequence Tags
  • Genome, Plant
  • Models, Genetic
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • RNA Precursors / genetics
  • RNA Precursors / metabolism
  • RNA Splice Sites
  • RNA, Plant / genetics
  • RNA, Plant / metabolism

Substances

  • RNA Precursors
  • RNA Splice Sites
  • RNA, Plant