Academic Journal
Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans
| العنوان: | Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans |
|---|---|
| المؤلفون: | Meng Li |
| المصدر: | BMC Bioinformatics, Vol 21, Iss 1, Pp 1-15 (2020) |
| بيانات النشر: | BMC, 2020. |
| سنة النشر: | 2020 |
| المجموعة: | LCC:Computer applications to medicine. Medical informatics LCC:Biology (General) |
| مصطلحات موضوعية: | Splicing, Intron splicing order, Most likely order, Bayesian network, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5 |
| الوصف: | Abstract Background Introns have been shown to be spliced in a defined order, and this order influences both alternative splicing regulation and splicing fidelity, but previous studies have only considered neighbouring introns. The detailed intron splicing order remains unknown. Results In this work, a method was developed that can calculate the intron splicing orders of all introns in each transcript. A simulation study showed that this method can accurately calculate intron splicing orders. I further applied this method to real S. pombe, fruit fly, Arabidopsis thaliana, and human sequencing datasets and found that intron splicing orders change from gene to gene and that humans contain more not in-order spliced transcripts than S. pombe, fruit fly and Arabidopsis thaliana. In addition, I reconfirmed that the first introns in humans are spliced slower than those in S. pombe, fruit fly, and Arabidopsis thaliana genome-widely. Both the calculated most likely orders and the method developed here are available on the web. Conclusions A novel computational method was developed to calculate the intron splicing orders and applied the method to real sequencing datasets. I obtained intron splicing orders for hundreds or thousands of genes in four organisms. I found humans contain more number of not in-order spliced transcripts. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1471-2105 |
| Relation: | http://link.springer.com/article/10.1186/s12859-020-03818-6; https://doaj.org/toc/1471-2105 |
| DOI: | 10.1186/s12859-020-03818-6 |
| URL الوصول: | https://doaj.org/article/985ce505ea0643d38fa33894a07cb331 |
| رقم الانضمام: | edsdoj.985ce505ea0643d38fa33894a07cb331 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 14712105 |
|---|---|
| DOI: | 10.1186/s12859-020-03818-6 |