Search tools | Browse the genomes | Download genomes and annotations | Gene expression atlases

Search tools at PeanutBase

  • BioProjects at NCBI ... to search NCBI's BioProject database for Arachis projects.
  • BLAST sequence search ... to search for your sequences using BLAST against the Arachis genomes, coding sequences, or peptides. Hits link to alignments or genes in the genome browsers.
  • BLAT sequence search ... to search for your sequences using BLAT ("Blast-Like Alignment Tool") against the Arachis genomes. BLAT is a tool for aligning gene/transcript sequences, or highly-similar DNA sequences, to a genome. May be better than BLAST for genic sequences that require spliced alignments around introns. Alignments will be displayed in the genome browser.
  • Browse Cultivated peanut using GBrowse
  • Browse A. duranensis using GBrowse or JBrowse
  • Browse A. ipaensis using GBrowse or JBrowse.
  • Gene expression atlases ... to explore Arachis gene expression atlases.
  • Genes and gene families search ... to search for legume genes and gene families and legume-focused gene trees (trees are maintained at partner site LegumeInfo). Manage sets of genes (collect protein or CDS sequences or descriptions) using the "basket" tool.
  • Germplasm search ... to search Arachis stock records.
  • Keyword search for sequence features ... to search in the selected genome for functional descriptions, gene names, marker names, etc.
  • Map search ... to search for maps available at PeanutBase - as well as associated information: parents, population, methods etc.
  • Marker search ... to search for markers and associated info: primers, sequences, associated maps, etc.
  • Protein domain search: Search for InterPro protein domains in genes
  • Publication search ... to search by author, year, keyword, title, abstract, etc. for publications for which QTL or map data has been collected.
  • QTL search ... to search for QTL features, including QTL names, symbols, associated publications, and other information about QTL mapping experiments.

Browse the genomes:

GBrowse viewer for Cultivated peanut ... or jump to a chromosome:
01 02 03 04 05 06 07 08 09 10
11 12 13 14 15 16 17 18 19 20
GBrowse viewers for Arachis duranensis or Arachis ipaensis ... or jump to a chromosome:
Aradu.A01 A02 A03 A04 A05 A06 A07 A08 A09 A10
Araip.B01 B02 B03 B04 B05 B06 B07 B08 B09 B10
JBrowse viewers for Arachis duranensis or Arachis ipaensis ... or jump to a chromosome:
Aradu.A01 A02 A03 A04 A05 A06 A07 A08 A09 A10
Araip.B01 B02 B03 B04 B05 B06 B07 B08 B09 B10

Download the genomes and annotations

Download the A. duranensis or Arachis ipaensis assemblies and annotations

Gene expression atlases

Tissue expression atlas: Comparison of RNA-Seq read counts from 22 Arachis hypogaea tissues against Arachis ipaensis and A. duranensis genomes combined. This analysis includes a table of counts of genes with differential expression from each tissue comparison. From differentially expressed genes, there are links to gene sequences, gene annotations, and views of expression in the genome browsers. This is the work of Dr. Peggy Ozias-Akins and colleagues.
Nematode expression experiment: Root transcriptome data for A. duranensis and A. stenosperma infected with Meloidogyne arenaria. Reference: Guimaraes PM, , et al. (2015) Root Transcriptome Analysis of Wild Peanut Reveals Candidate Genes for Nematode Resistance. PLoS ONE 10(10): e0140937). (PubMed).
Drought expression experiment: Comparison of RNA-Seq read counts from A. duranensis and A. stenosperma under drought treatment and control conditions. Data from Ana Cristina Miranda Brasileiro and Patricia Guimaraes (ms. in preparation). Please contact the authors prior to using this data.