ArchaeProfile: A Database of Archaea and their Origins of Replication

Abstract

Archaea are single cell microorganisms having several unique characteristics which differentiate them from bacteria. One of the key features which make archaea distinct from bacteria is the replication process, which is very different and resembles that of the eukaryotes. In-vivo mapping of the ori site in Archae is a time consuming and tedious job due to complexity involved in the culture of archaeal colony, which puts challenges as well as opportunity to scientist to devise in-silico method to map the Ori site in archaeal genomes. Z-curve approach is a widely used insilico method to predict the Ori site in archaea, but it is not equally successful for all archaeal genomes. Several other parameters like copy number and location of the cdc6 gene, AT rich region with the presence of origin recognition boxes (ORB) provide a better estimate of the Ori site in archaea. The motivation behind development of Archae Profile database is to predict the location and the number of putative Ori sites in archaeal genomes based on purinepyrimidine(R-Y) and amino-keto(M-K) disparity curve along with the consensus ORB sequences, cdc6 gene copy number, their location and upstream AT richness. Quick update cycle and easy browser interface makes Archae Profile distinct from other databases. Another important feature is the integration of tools for plotting disparity plot of a given genome sequence and finding specific repeats with copy number and location in a sequence. ArchaeProfile will be updated timely and the emphasis will be to integrate other tools for genome analysis as well as new search features in the database. Presently Archaea Profile has Ori related data of 122 archeal genome which is likely to increase with time.Availability: ArchaeProfile can be accessed freely from http://www.bioinfommv.in/archaeprofile. Data available on the database could be used for further analysis and tutorial purpose. Furthermore a tool has also been incorporated within the database which can draw the nucleotide skew plot of the nucleotide sequence supplied by users. Another tool which is helpful in finding specific repeats and their position in nucleotide sequence, is also given in the database, this can be useful in detecting short and long repeats in the Ori site in archaeal genomes which are very common [10,11]. Genes associated with the origin of replication in archaea like cdc6 with the full description of the location and the copy number of the above genes is also available on the database, as the association of cdc6 gene with the change in sign of the of disparity curve is a good indicator to find Ori site in archaeal genomes. Further the location of Origin Recognition Boxes (ORB) is necessary as a confirmation of the detection of the Ori site in Archae [12]. In Archae Profile database we have given all experimentally verified ORB's as well as in-silico predicted consensus ORB sequences and their location. The consensus ORB sequences were generated by multiple sequence alignment of predicted Ori region of closely related arche...