Some of our recent research has involved using our CEGMA software pipeline to study the many whole genome shotgun (WGS) genome sequences that are being produced. In a recently submitted manuscript that looks at the utility and completeness of WGS genomes, we have shown that the genome annotations that accompany genome sequences frequently miss important, and highly-conserved genes. As a free service, we will run our CEGMA pipeline software against any (eukaryotic) genome sequence to:
Please email korflab @ ucdavis.edu for more information.
A Perl module that makes it easy to process FASTA formatted files
A web tool to calculate the enhancing ability of any specified intron sequence. You can also download a command-line version of this tool.
Core Eukaryotic Genes Mapping Approach. Software and datasets provided.
Using CEGMA to investigate utility of draft genome sequences
Datasets and software used for our Bind-N-Seq paper, a method that uses short read sequencing to analyze protein-DNA interactions.
(Semi-HMM-based Nucleic Acid Parser) gene prediction tool.
Gene Neighborhood Scoring Tool. To access, under "Tools," click on "ucdavis" then "gnest"
This file is a tar.gz file containing Perl scripts that comprise the Sole Search software, and a README file. Please see the associated publication for more information.
An easy to use hidden Markov model-based copy number variant identifier.
Mar 23, 2011: A Nature news article about genome assembly, with an interview of Ian Korf.
For questions or comments about the website, please e-mail:
korflab AT ucdavis DOT edu
Contact information for specific members of our lab can be found on their personal pages.