Integration of and Access to Distributed Data and Tools in Genomics

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