OREGON STATE UNIVERSITY

SERVICES

The CGRB Bioinformatics group provide services to researchers working around the world. Please look at our CGRB Core Labs website for details.

This page showcases select resources hosted by CGBI participants.

Public Resources

ASRP Database The Arabidopsis Small RNA Project seeks to characterize and functionally analyze the two major classes of endogenous small RNAs - microRNAs (miRNAs) and short-interferring RNAs (siRNAs).
Brachypodium.org The Brachypodium distachyon model grass portal.
Personal Sequence Database (PSD) The PSD project provides a set of tools to create and maintain web-accessible sequence databases. PSD databases can be privately maintained or published to the web and queried by keyword or sequence similarity using NCBI BLAST. Methods exist for bulk import and export as well as alerting users to new BLAST hits in public databases.
TargetFinder Targetfinder predicts small RNA targets in a sequence database using a plant-based scoring metric. Click link to download gzipped perl script.
CASHX The CASHX Pipeline is used to process short read data output from Illumina and other HTS technologies. The pipeline can be used to parse, map, qauntify and manage large quanities of sequence data.

Restricted Access Software

ETA The Easy Terminal Alternative will replace the BioInfo site for the CGRB. This includes tools developed at the CGRB such as the Personal Sequence Database and SeqTool, as well as externally developed tools such as BLAST, FASTA, ClustalW, T-Coffee, MUSCLE, CAP3, Primer3 and the EMBOSS suite.
Genome Cluster Status Monitor the activity of the Genome cluster.