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 in over 30 plant species. 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.
Mar 16, 2015: Danielle Lemay is interviewed by the UC Davis News team about the new publication by herself, Kristen Beck (lead author), Ian Korf and others that describes new milk proteomes for human and macaque.
Apr 22, 2013: The Assemblathon 2 paper has won the 2013 BioMed Central Open Data award
Dec 10, 2013: A short piece in the UC Davis Alumni Magazine that discusses the new Genomics undergraduate major that Ian Korf co-developed.
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)
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.