The Design and Implemention of Updating and Monitoring Alternative Splicing Database
| Autor: | chin-feng Chen, 陳金風 |
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| Rok vydání: | 2005 |
| Druh dokumentu: | 學位論文 ; thesis |
| Popis: | 93 Alternative splicing (AS) is an important mechanism of gene expression in eukaryotic cells. It needs a huge amount of calculations and complex procedures to construct AS database. We know that two main materials will be added and revised and they are expressed as sequence tag sequence (ESTs) and genome. The dbEST has an increase in hundred thousand ESTs every month on average, including different species (humans, and mice etc.). The genome upgrades the edition and emerges in approximately once half a year. If genome upgrades, it needs a large amount of EST aligned to genome and ESTs should be grouped by exon. Then, we parser EST’s exon belongs to what form of alternative splicing. It is quite time-consuming to carry out these procedures. Six million ESTs take a month to finish this job by ten personal computers. Maintenance and surveillance of the updated accuracy of the AS database requires manpower. In order to solve this problem, the AS database possesses renewed capability (offering individualized instant information to users). In other words, we check unusual fluctuations only within a cycle and update the AS database. So, we have developed updated procedures to help carry out this complicated work. At the same time, it offers those differences in the new alternative splicing database to users, which may be an interesting part for readers. Homo sapiens genome sequences are almost finished. Homo sapiens genome sequences do not modify over 90% of them. If ESTs on these sequences without modifies prolong and use the result of last time, alignment time will be saved. We have explained the approach of using the genome sequences location to reduce time of aligning expressed sequence tags (ESTs) with genome. There are only some differences in different genomic editions. Most ESTs only need to use the last result of all ESTs aligning genome. In other words, we can get the same position of ESTs aligning the genome position without change. If genome is updated, all ESTs align new genome again in the traditional way. We have saved 90% of the time by utilizing genome position. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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