KoriBlast can be connected to an exisiting Blast system, or we can deploy one for you. In all cases, we have to provide you with an additional software package to install on your side: the KoriBlast Server.

The KoriBlast Data Server

KBServer (KoriBlast Server) is a J2EE programme used to distribute Blast jobs on a computational intensive infrastructure.

KBServer can perform:

• the launch of Blast jobs on distributed infrasctructure,
• the integration of sequence data (i.e. feature tables, biological classifications, etc.) within Blast results, i.e. producing fully annotated Blast results.

The server is provided with a standalone release of the Korilog Databank Manager System (KDMS). KDMS is a programme used to locally install sequence databases compliant with Fasta, as well as standard annotated sequence formats: Genbank, Genpept, Uniprot and Embl. The software is also capable of installing several biological classifications that are used during the annotation step mentioned above. These classifications are: NCBI Taxonomy, Gene Ontology, InterPro, PFam and Enzyme.

KDMS automatically performs:

• the download of the database files from remote sites (via FTP),
• the decompression of the files (gzip files),
• the un-archiving of the files (tar files),
• the conversion of native sequence files to Fasta ones,
• the preparation of databases in BLAST format from Fasta files,
• indexing of Genbank, Genpept, Embl and Uniprot files allowing their efficient querying by way of sequence identifiers,
• indexing of biological classifications allowing their efficient querying by way of classification identifiers.

KDMS can be used from the Unix command-line or a graphical user interface (see screenshot). Using command-line script enables the use of 'cron' to schedule databank installations over time.

Screenshot of the Databank Manager available with the KoriBlast Server

System requirements

KBServer has been tested with the following operating systems:

• Redhat Linux Fedora Core 7 and 10
• MacOS X (10.6 and 10.7)

on an Intel/Pentium platform (dual & quadri cores). It is advised to have at least 1024MB of RAM.

KBServer uses the following systems:

• an Oracle Java virtual machine, version 1.6 or higher
• an Apache Tomcat server, version 6.x

KBServer by itself can use a default mode where it can fully handle batch jobs scheduling. It is worth noting that in this mode, KBServer runs all jobs on the computer running it, i.e. on the Tomcat server.

To go further in job scheduling, KBServer can be configured to use OGE (Oracle Grid Engine, that used to be called Sun Grid Engine) or PBS Pro. KBServer has been tested with SGE 6.0, 6.1 and 6.2 and PBS Pro 10.4.

KBServer comes with the standard NCBI Blast software. However, it is possible to configure the system to use other Blast binaries, e.g. mpi-Blast.

Screenshot of the KoriBlast Server administration interface

Need more informations ?

Please contact us to get more information about the KoriBlast Server.