ORIS

We have implemented various existing methods in the context of replication origin finding and also incorporated few new measures which are hitherto not part of any freely available origin finding software tool. Software modules are offered and arranged in a contextual view and simple visualisation plots are provided to aid in making useful inferences. Our software suite called ORIS stands for ORIgin Search and is meant to help researchers in identifying origin of replication sites in the genomic data of prokaryotes, archea and eukaryotes. Our java based software package is free and has many modules which deal with GC and AT skew, cumulative skew, autocorrelation, cross-correlation, origin specific motif search with mismatches, weight matrix search, Shannon and Renyi entropy and bending profiles. ORIS also supports userdefined expressions which can be very useful in the discovery of new methods for predicting replication origin ORIS is written in java language. it was chosen because of its features like object oriented, platform independent, architecturally neutral, robust, multithreaded etc (10). ORIS has a java swing based GUI. As it is implemented in java, any machine with any operating system having JRE (Java Runtime Environment) can run ORIS.

ORIS : Description

A remarkable yet very precise event that takes place within the cell , is called DNA replication or chromosome copy (2). The way it is done in eukaryotes is vastly different from prokaryotes yet something is common as well. Molecular replication machinery is complex and very less is understood in terms of its structure and function (3). The binding of Origin Recognition Complex protein (ORC) enables recruitment of the recognition complexes such as Cdcs and Mcms(mini chromosome maintenance) to carry out the process. In simple terms, the origin of replication is a sequence in the genome at which the replication process is initiated. Bacterial genomes generally have a single origin of DNA replication whereas eukaryotes have multiple replication sites and this organizational structure may be needed to complete the replication task within the single ’S’ phase of the cell cycle(4,5). Experimental studies carried out on the model organism S. cerevisiae brought out greater insights in understanding the complex replication process. A typical origin sequence in S. cerevisiae has a DNA segment called ’Autonomous Replication Sequence (ARS)’ and this further has an essential ’A’ element and multiple ’B’ elements and all these are required for proper origin function or firing. This kind of organizational structure may be there in other eukaryotic genome sequences but they are not very obvious. And we will have to exploit this contextual information as part of our computational searches.

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