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 use this page to submit CEGMA requests to us
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 - latest release 11/29/2013.
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.
Nov 26, 2013: Ian Korf writes a News & Views piece for Nature Methods about two new comparisons of programs that work with RNA-seq data
Sep 24, 2013: An article on genome assembly by My Science Work includes an interview with Keith Bradnam about Assemblathon 2 & 3.
Aug 12, 2013: Biome Magazine includes a piece that features Ian Korf discussing a novel platform for bioinformatics education (with Daniel Barker)
Jul 22, 2013: The News blog at Nature.com writes about the Assemblathon 2 paper.
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.