The Prediction of Rice Gene by Fgenesh

ZHANG Sheng-li; LI Dong-fang; ZHANG Gai-sheng; WANG Jun-wei; NIU Na

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The Prediction of Rice Gene by Fgenesh

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This study has been carried out to give some scientific reasons for genome annotation, shorten the annotating time, and improve the results of gene prediction. Taking the sequence of the 6th chromosome, which has more length sequences than others, of Oryza sativa L. ssp. japonica cv. Nipponbare as analysis data in this research, the gene prediction of monocots module, rice, has been done by using Fgenesh ver. 2.0, and the predicting results have been explored particularly by bioinformatics methods. Results showed that the number of predicted genes for this chromosome was very close to the number of TIGR annotated genes. The majority of the predicted genes were multi-exon genes which had a percentage of 77.52. Length range was very big in the predicted genes. According to the significant match number, multi-exon genes can be predicted more veracity than single exon genes and the support can be reached up to 100% by TIGR annotation and up to 78% by cDNA. From the angle of predicted exons location of multi-exon genes, the internal exons and last exons had a high support of cDNA. The length of internal exons was relatively short in high (> 95% length, > 78% similarity) cDNA and/or TIGR annotation support multi-exon genes, but the first exons and last exons were on the reverse. The majority of single exon genes which had more than 95% in length, and 78% in similarity support by cDNA and/or TIGR annotation was relatively short in length. From the angle of exon number, the majority of the multi-exon genes of high (> 95% length, > 78% similarity) cDNA and/or TIGR annotation support had no more than 5 exon number. It was concluded that the rice gene prediction by Fgenesh was very good but needed modification manually to some extent according to cDNA support after aligning the predicting sequence of genes with cDNA database of rice.

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《农业科学学报：英文版》 |2008年第4期|387-394|共8页
作者
ZHANG Sheng-li; LI Dong-fang; ZHANG Gai-sheng; WANG Jun-wei; NIU Na;
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作者单位

Shaanxi Key Laboratory of Crop Heterosis;

Northwest A ＆ F University;

Yangling 712100;

P.R. China;

Key Discipline Open Laboratory on Crop Molecular Breeding;

Henan Institute of Higher Learning/Henan Institute of Science andTechnology;

Xinxiang 453003;

P.R.China;

School of Resources and Environmental Sciences;

Henan Institute of Science and Technology;

Xinxiang 453003;

P.R.China;

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原文格式 PDF
正文语种 chi
中图分类稻;
关键词
cDNA; 稻米; 基因检测; 外显子;

机译：水稻;基因预测;cDNA;注释;外显子;

The Prediction of Rice Gene by Fgenesh

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