• Genome Browser
  interactively visualize genomic data
• BLAT
  rapidly align sequences to the genome
• Table Browser
  download data from the Genome Browser database
• Variant Annotation Integrator
  get functional effect predictions for variant calls
• Data Integrator
  combine data sources from the Genome Browser database
• Gene Sorter
  find genes that are similar by expression and other metrics
• Genome Browser in a Box (GBiB)
  run the Genome Browser on your laptop or server
• In-Silico PCR
  rapidly align PCR primer pairs to the genome
• LiftOver
  convert genome coordinates between assemblies
• VisiGene
  interactively view in situ images of mouse and frog

More tools...

Eukaryotic chromosomes consist of DNA-protein complexes referred to as chromatin. Understanding of the relationship between chromatin structure and genome behavior is a long term goal of this project (NSF 1444532). Our immediate aim is to identify and map genome-wide changes in chromatin structure using nuclease sensitivity profiling in five diverse tissues of maize. Biochemically defined DNS-seq profiles serve to integrate genetic, genomic, and epigenomic information.

GENOMAIZE.ORG was developed Daniel Vera, Katie Kyle, and Hank Bass using the UCSC browser and is hosted by FSU's Dept. of Biological Science. More information about the NUPRIME project is available at maizenucleosome.org.

Maize DNS/Differential Nuclease Sensitivity References:

1st genome-wide DNS profiling in a multicellular organism:
(2014) Vera et al. Plant Cell 26(10):3883-3893. (DOI: 10.1105/tpc.114.130609).

GWAS with DNS-seq functional genomics:
(2016) Rodgers-Melnick et al. PNAS 113(22):E3177-E3184 (DOI: 10.1073/pnas.1525244113).

iSeg, a new peak-calling algorithm for genomic data:
(2018) Girimurugan et al. BMC Bioinformatics 19:131 (DOI: 10.1186/s12859-018-2140-3).

Maize B73 DNS-seq profiles of 4 core tissues:
SRA at NCBI BioProject Acc: PRJNA445708 (2018) Turpin et al., Data in Brief August 2018 (DOI: 10.1016/j.dib.2018.08.015).