Record Details

Determination of window size and identification of suitable method for prediction of donor splice sites in rice (Oryza sativa) genome

KRISHI: Publication and Data Inventory Repository

View Archive Info
 
 
Field Value
 
Title Determination of window size and identification of suitable method for prediction of donor splice sites in rice (Oryza sativa) genome
Not Available
 
Creator Prabina Kumar Meher
Tanmaya Kumar Sahu
A. R. Rao
S. D. Wahi
 
Subject Splice sites
Prediction accuracy
Window size
Short sequence motif
 
Description Not Available
Accurate prediction of the gene structure depends upon the accurate prediction of splice sites. The conserved feature in splicing junction has been successfully used for the prediction of eukaryotic splice sites. In eukaryotes, though the di-nucleotide GT is conserved at 5′ splice sites, the pattern surrounding the conserved di-nucleotide varies from species to species. Most of the work related to splice site analysis has been extensively done in Homo sapiens and Arabidopsis thaliana. However, such works are yet to be fully explored in Oryza sativa and other species of grass family. In this study, statistical techniques have been applied to discriminate the real splice sites from pseudo splice sites in rice, maize and barley genomes and based on this a suitable window size is determined for the prediction of donor splice sites. Depending upon the determined window size, appropriate methods for predicting donor splice sites in rice have been considered and compared in terms of prediction accuracy. The results revealed that a window size of 9 base pair (3 bp at the exon end and 6 bp at the intron start including the conserved di-nucleotide GT at the beginning of intron) is an effective window size in all the three species of grass family for the prediction of donor splice sites. Further, the Maximum Entropy Model based method is found as best among the short sequence based prediction methods for donor splice sites with the 9 base pair window size.
Not Available
 
Date 2022-08-07T07:53:04Z
2022-08-07T07:53:04Z
2014-11-18
 
Type Research Paper
 
Identifier Prabina Kumar Meher, Tanmaya Kumar Sahu, A. R. Rao, S. D. Wahi (2015). Determination of window size and identification of suitable method for prediction of donor splice sites in rice (Oryza sativa) genome, Journal of Plant Biochemistry and Biotechnology, 24(4), 385-92.
Not Available
http://krishi.icar.gov.in/jspui/handle/123456789/73740
 
Language English
 
Relation Not Available;
 
Publisher Not Available