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Protocols

PeanutBase specifications

Information


Unique identifier OMICS_32157
Name PeanutBase
Alternative name Peanut Genome Project
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Additional information


https://peanutbase.org/help

Publication for PeanutBase

PeanutBase citations

 (25)
library_books

High Density Genetic Map Construction and Identification of QTLs Controlling Oleic and Linoleic Acid in Peanut using SLAF seq and SSRs

2018
Sci Rep
PMCID: 5883025
PMID: 29615772
DOI: 10.1038/s41598-018-23873-7

[…] Comparing with the reference genome (http://peanutbase.org/home), HighMap assigned 2,334 of 2,384 markers to 20 LGs of peanut including 2,266 SNPs and 68 SSRs. The total genetic length of the molecular linkage map was 2,586.37 cM in twenty link […]

library_books

Genome Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis

2017
Front Plant Sci
PMCID: 5742254
PMID: 29312366
DOI: 10.3389/fpls.2017.02064

[…] A. ipaënsis (accession K30076 for B subgenome,) were used for mining the InDels using the methodology depicted by Yang et al. (). Briefly, the fasta files for A and B subgenomes were downloaded from PeanutBase site (https://www.peanutbase.org/) and InDels were identified using MUGSY software (Angiuoli and Salzberg, ). The alignment results were mined for InDel polymorphism using the Perl scripts […]

library_books

Isolation and functional analysis of fatty acid desaturase genes from peanut (Arachis hypogaea L.)

2017
PLoS One
PMCID: 5731756
PMID: 29244878
DOI: 10.1371/journal.pone.0189759

[…] Homologs of each member of the Arabidopsis FAD family were identified by BLASTP searches with datasets from Phytozome v10.3 (www.phytozome.net) and Peanut Genome Project (http://peanutbase.org/home) []. Only those sequences with an e-value less than e−50 were considered as members of the FAD family. In each tree, gene sequences were displayed usi […]

call_split

Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs

2017
Sci Rep
PMCID: 5665869
PMID: 29093502
DOI: 10.1038/s41598-017-13981-1
call_split See protocol

[…] The A. duranensis and A. ipaënsis CDSs were downloaded from PeanutBase (http://peanutbase.org/download). To avoid including partial sequences in these analyses, the following evaluation criteria were adopted: (1) CDSs were required to start with an ATG codon a […]

library_books

Genome wide analysis of basic/helix loop helix gene family in peanut and assessment of its roles in pod development

2017
PLoS One
PMCID: 5531549
PMID: 28750081
DOI: 10.1371/journal.pone.0181843

[…] The whole genome sequence of the peanut AA-subgenome (Aradu.V14167.a1.M1) and BB-subgenome (Araip.K30076.a1.M1) were obtained from PeanutBase (http://peanutbase.org/) and the HMM sequence of the bHLH domain (PF00010) was downloaded from the pfam database (http://pfam.xfam.org/) and used as query to search for candidate peanut bHL […]

call_split

Genome Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea)

2017
Front Plant Sci
PMCID: 5513918
PMID: 28769940
DOI: 10.3389/fpls.2017.01209
call_split See protocol

[…] The whole genome sequences of A. duranensis and A. ipaensis were downloaded from PeanutBase. The genome sequences were used to identify SSR loci using Perl scripts software MISA with the default parameters. The identification criteria were: mono-nucleotide repeats motif with at le […]

Citations

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PeanutBase institution(s)
National Center for Genome Resources, Santa Fe, NM, USA; Department of Computer Science, Iowa State University, Ames, IA, USA; USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA, USA
PeanutBase funding source(s)
Supported by The Peanut Foundation and USDA-ARS.

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