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Integration of and Access to Distributed Data and Tools in Genomics

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Integration of and Access to Distributed Data and Tools in Genomics

Sadrarhami, Hajar (2011) Integration of and Access to Distributed Data and Tools in Genomics. Masters thesis, Concordia University.

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Abstract

One of the important data sources in bioinformatics is protein or nucleotide sequences that are used as input to many programs to collectively or individually analyze them. There exists an ample amount of protein sequences scattered over many different databases. This division complicates the process of feeding them into existing programs to be further analyzed. Moreover, there exists a program integration portal, namely Mobyle that makes the common programs available with unified interface to the users; in addition, it provides the functionality of chaining the results from one program to another. The two existing programs in Mobyle fetch sequences to feed the other programs, however, they fetch sequences from limited number of databases that are statically defined by the Mobyle administrator. In addition, neither of these tools have access to the DAS servers, resulting in the loss of a major data source. In this work, a program was developed and integrated, namely DasSeqFetcher, for use in Mobyle to dynamically fetch sequences from all available sequence databases providing a DAS reference server. Also, both DAS reference and annotation servers were developed for a database made by our research group which holds experimentally characterized lignocellulose-active proteins. The reference servers can then be added to DAS registry to be used by DAS client tools, e.g. DasSeqFetcher.

Divisions:Concordia University > Faculty of Engineering and Computer Science > Computer Science and Software Engineering
Item Type:Thesis (Masters)
Authors:Sadrarhami, Hajar
Institution:Concordia University
Degree Name:M. Comp. Sc.
Program:Computer Science
Date:15 April 2011
Thesis Supervisor(s):Butler, Gregory
ID Code:7380
Deposited By:HAJAR SADRARHAMI
Deposited On:15 Jun 2011 09:32
Last Modified:10 Jan 2012 08:29

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  • Integration of and Access to Distributed Data and Tools in Genomics. (deposited 15 Jun 2011 09:32) [Currently Displayed]
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