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:
- assess how many genes are likely to be present/absent in that assembly and
- accurately predict the structures of a set of conserved genes that we believe are present in all eukaryotes.
Please email korflab @ ucdavis.edu for more information.
Korf Lab - Software & Databases
FAlite.pm
A Perl module that makes it easy to process FASTA formatted files
IMEter
A web tool to calculate the enhancing ability of any specified intron sequence. 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.
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.
Korflab in the news
Jan 28, 2013: A Haldane's Sieve Blog Post by Keith Bradnam that discusses the Assemblathon 2 pre-print
Nov 12, 2012: a feature on Danielle Lemay by the Calfifornia Dairy Research Foundation
Mar 23, 2011: A Nature news article about genome assembly, with an interview of Ian Korf.
Quick Links
Unix & Perl for Biologists
Our free 175-page primer that teaches the basics of Unix & Perl
Unix & Perl to the RESCUE!
Our book that greatly expands on our free primer.
Software GALAXY
Comprehensive online toolkit for sequence analysis and visualisation
UC Davis Genome Center
Where we work
UC Davis Bioinformatics Core
Part of the Genome Center
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.