About Korf Lab

Software & Data

We can help you!

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

Korf Lab - Software & Databases

FAlite.pm

A Perl module that makes it easy to process FASTA formatted files

IMEter v2.1

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.

CEGMA

Core Eukaryotic Genes Mapping Approach. Software and datasets provided.

Genome completeness

Using CEGMA to investigate utility of draft genome sequences

BindNSeq

Datasets and software used for our Bind-N-Seq paper, a method that uses short read sequencing to analyze protein-DNA interactions.

SNAP

(Semi-HMM-based Nucleic Acid Parser) gene prediction tool - latest release 11/29/2013.

G-NEST

Gene Neighborhood Scoring Tool. To access, under "Tools," click on "ucdavis" then "gnest"

MPBLAST

Multiplex BLAST

Sole-SearchV2.tar.gz

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.

DupHMM

An easy to use hidden Markov model-based copy number variant identifier.

About Korf Lab

Korf Lab in the news

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


Nov 1, 2013: Keith B. and Kristen are both featured in a piece on Inquiring Minds as part of the new One UC Davis campaign.


Nov 1, 2013: Kristen made a list of the Top 10 moments of the IMGC symposium for the SPLASH! newsletter


Oct 1, 2013: The new paper by Lemay et al., was featured in This Week in PLOS by Genome Web.


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)


Aug 8, 2013: Biome, the online magazine for BioMed Central, features an extensive Q&A with Keith Bradnam about the Assemblathon 2 paper.


Jul 22, 2013: The News blog at Nature.com writes about the Assemblathon 2 paper.

More news

Contact Us

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.