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Search results 501 to 525 out of 525 for *

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Category: DataSet
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Type Details Score
Data Set
mixed.map.GmSSR-SIU
URL: https://data.legumeinfo.org/Glycine/max/maps/mixed.map.GmSSR-SIU/
Description: Consensus genetic map GmSSR-SIU drawn from SoyBase.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
mixed.map.GmSSR-Utah
URL: https://data.legumeinfo.org/Glycine/max/maps/mixed.map.GmSSR-Utah/
Description: Consensus genetic map GmSSR-Utah drawn from SoyBase.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
mixed.map.GmSSR-Utah2
URL: https://data.legumeinfo.org/Glycine/max/maps/mixed.map.GmSSR-Utah2/
Description: Consensus genetic map GmSSR-Utah2 drawn from SoyBase.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
mixed.map.GmSSR-Utah3
URL: https://data.legumeinfo.org/Glycine/max/maps/mixed.map.GmSSR-Utah3/
Description: Consensus genetic map GmSSR-Utah3 drawn from SoyBase.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
mixed.map.GmUSDA1997
URL: https://data.legumeinfo.org/Glycine/max/maps/mixed.map.GmUSDA1997/
Description: Consensus genetic map GmUSDA1997 drawn from SoyBase.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
Gene Ontology
URL: http://www.geneontology.org
Description: The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
Licence: https://creativecommons.org/licenses/by/4.0/
DataSource: Gene Ontology
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Data Set
legume.genefam.fam1.M65K
URL: https://data.legumeinfo.org/LEGUMES/Fabaceae/genefamilies/legume.genefam.fam1.M65K/
Description: Files in this directory include the main results for gene families constructed for the legume family. Methods are documented at https://github.com/LegumeFederation/legfed_gene_families. Briefly, the methods are based on gene pairs filtered for per-species Ks values. These were clustered using Markov clustering. Sequence match scores of each sequence in a family were used to identify outliers, on the basis of score value relative to the median score for the family. Remaining sequences were re-clustered, added to the HMM set. Then all sequences were searched against all HMMs, realigned, re-screened relative to median match score, and finally used to generate alignments and phylogenetic trees (using RAxML). The trees are rooted, when possible, using the closest outgroup from among five outgroup species: Arabidopsis thaliana, Prunus persica, Cucumis sativa, Solanum lycopersicum, and Vitis vinifera.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
InterPro data set
   
Description: InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
DataSource: InterPro
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Data Set
InterPro domain GO annotations
   
Description: Mapping of GO terms to InterPro entries.
DataSource: InterPro
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Data Set
pfamA.txt
 
URL: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/database_files/
Description: Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
DataSource: EMBL-EBI
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Data Set
PANTHER17.0_HMM_classifications
 
URL: http://data.pantherdb.org/ftp/hmm_classifications/current_release/
Description: PANTHER HMM Classification file. Contains the PANTHER family/subfamily name, and the molecular function, biological process, and pathway classifications for every PANTHER protein family and subfamily in the PANTHER HMM library.
DataSource: PANTHER
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Data Set
Wm82.gnm5.NRKG
URL: https://data.legumeinfo.org/Glycine/max/genomes/Wm82.gnm5.NRKG/
Description: Sequenced using PacBio RSII and HiFi reads, with Bionano optical maps to aid in scaffolding. See full description at Garg, Khan et al., 2023.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
Wm82_NJAU.gnm1.N4GV
URL: https://data.legumeinfo.org/Glycine/max/genomes/Wm82_NJAU.gnm1.N4GV/
Description: Sequenced using PacBio HiFi, Nanopore ONT ulta-long, and short read Illumina sequencing; assembled with hifisam v0.16.1; minimap2 v2.24; Racon v1.5.0; RagTag v2.1.0
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
Wm82_NJAU.gnm1.ann1.KM71
URL: https://data.legumeinfo.org/Glycine/max/annotations/Wm82_NJAU.gnm1.ann1.KM71/
Description: Gene annotation resources. See full description in supplemental methods at Wang, Lomngfei et al., 2023
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
mixed.gwas.Wang_Chu_2016
URL: https://data.legumeinfo.org/Glycine/max/gwas/mixed.gwas.Wang_Chu_2016/
Description: We developed a high-throughput NJAU 355K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
Kefeng1_x_Nannon1138-2.qtl.Du_Wang_2009
URL: https://data.legumeinfo.org/Glycine/max/qtl/Kefeng1_x_Nannon1138-2.qtl.Du_Wang_2009/
Description: Further information provided in 10.1016/s1673-8527(08)60165-4
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
PI27890_x_PI290136.qtl.Mansur_Lark_1993
URL: https://data.legumeinfo.org/Glycine/max/qtl/PI27890_x_PI290136.qtl.Mansur_Lark_1993/
Description: Further information provided in 10.1007/BF00211040
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
PI437654_x_BSR101.qtl.Webb_Baltazar_1995
URL: https://data.legumeinfo.org/Glycine/max/qtl/PI437654_x_BSR101.qtl.Webb_Baltazar_1995/
Description: Further information provided in 10.1007/bf00223282
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
InterMine intergenic regions
 
URL: http://www.intermine.org
Description: Intergenic regions created by the InterMine core post-processor
DataSource: InterMine post-processor
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Data Set
Glycine.pan4.RK4P
URL: https://data.legumeinfo.org/Glycine/GENUS/pangenes/Glycine.pan4.RK4P/
Description: Pan-gene set for Glycine species, spanning 8 species and 51 annotation sets, calculated using the pandagma pipeline, version 2023-09-15
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
InterMine intergenic regions
 
URL: http://www.intermine.org
Description: Intergenic regions created by the InterMine core post-processor
DataSource: InterMine post-processor
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Data Set
Zhutwinning2.gnm1.ann1.ZTTQ
URL: https://data.legumeinfo.org/Glycine/max/annotations/Zhutwinning2.gnm1.ann1.ZTTQ/
Description: Gene annotations for Glycine max accession Zhutwinning2 (SoyL01) from Liu, Du et al. 2020. Annotations of the protein-coding and small RNA genes employed Augustus trained by FGENESH, transcript support based on RNA samples from roots, stems, leaves, flowers, and seeds at different developmental stages;and integration of ab initio and evidence-based results with MAKER.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
InterMine intergenic regions
 
URL: http://www.intermine.org
Description: Intergenic regions created by the InterMine core post-processor
DataSource: InterMine post-processor
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Data Set
Wm82.gnm5.ann1.J7HW
URL: https://data.legumeinfo.org/Glycine/max/annotations/Wm82.gnm5.ann1.J7HW/
Description: Gene annotation resources. See full description at Garg, Khan et al., 2023.
Licence: ODC Public Domain Dedication and Licence (PDDL)
DataSource: LIS Datastore
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Data Set
InterMine gene-flanking regions
 
URL: http://www.intermine.org
Description: Gene-flanking regions created by the core InterMine post-processor
DataSource: InterMine post-processor
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USDA
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