DNA replication is one of the most basic processes in all three domains of 
cellular life. With the advent of the post-genomic era, the increasing number of 
complete archaeal genomes has created an opportunity for exploration of the 
molecular mechanisms for initiating cellular DNA replication by in vivo 
experiments as well as in silico analysis. However, the location of replication 
origins (oriCs) in many sequenced archaeal genomes remains unknown. We present a 
web-based tool Ori-Finder 2 to predict oriCs in the archaeal genomes 
automatically, based on the integrated method comprising the analysis of base 
composition asymmetry using the Z-curve method, the distribution of origin 
recognition boxes identified by FIMO tool, and the occurrence of genes 
frequently close to oriCs. The web server is also able to analyze the 
unannotated genome sequences by integrating with gene prediction pipelines and 
BLAST software for gene identification and function annotation. The result of 
the predicted oriCs is displayed as an HTML table, which offers an intuitive way 
to browse the result in graphical and tabular form. The software presented here 
is accurate for the genomes with single oriC, but it does not necessarily find 
all the origins of replication for the genomes with multiple oriCs. Ori-Finder 2 
aims to become a useful platform for the identification and analysis of oriCs in 
the archaeal genomes, which would provide insight into the replication 
mechanisms in archaea. The web server is freely available at 
http://tubic.tju.edu.cn/Ori-Finder2/.