Bioinformatics

Tripal is a collection of open-source freely available Drupal modules under development at CUGI. These modules serve as a web interface for the GMOD Chado database. Tripal is a part of the GMOD family of tools.

CUGI's bioinformatics staff is available to perform basic and customized analysis of ESTs ranging from pre-processing and assembly to functional annotation.

As an extension to our shotgun library construction and sequencing services, CUGI offers assembly, gap closure and finishing of whole BACs. Sequence data may be generated at CUGI from an external sequencing facility.

A combination of in-house scripts and publicly available software applications have been developed to mine SSRs and SNPs from Sanger-style or next generation sequence sets.

A strength of CUGI bioinfomatics is in the area of construction and management of online genomic databases.

CUGI specializes in physical mapping via High-information Content Fingerprinting (HICF). Our bioinformatics staff has experience in assembling and analyzing HICF fragment data to construct high quality physical maps.

CUGI bioinformaticists have experience assembling short reads from genomic DNA and ESTs.

An in-house pipeline has been constructed at CUGI for the Quality Analysis (QA) and Trimming of Sanger-style genomic and transcriptomic data.