Analysis Search
| Name Sort descending | Description | Data Source Name | Software Name | Algorithm | Date and Time Executed | |
|---|---|---|---|---|---|---|
| 10.1002/csc2.20333 Relatedness and heritability of carrot CWR germplasm accessions | Sixty-five of the accessions included in this study had been genotyped as part of a project to characterize carrot germplasm and develop genetic resources for cultivar improvement. These 65 accessions were genotyped using genotyping-by… |
10.1002/csc2.20333 | TASSEL-GBS+Beagle+adegenet+hiefstat+GAPIT | |||
| 10.1080/13102818.2019.1701551 2019 SSR | A published collection of 55,386 SSR primer pairs. GMATA (Genome-wide Microsatellite Analyzing Tool Package) software was utilized for mining the genome assembly https://www.ncbi… |
figshare_8593337_2 | GMATA | |||
| 10.1534/g3.117.043067 Transcriptome Analysis for Y₂ | Carrot root tissue was collected from three yellow (yyY2Y2) and three orange (yyy2y2) pigmented biological replicates, plants from the progenitor F2 population of population 74,146, at 40 (time… |
10.1534/g3.117.043067 | Bowtie; Tophat; Cufflinks | |||
| 10.3390/ijms22189713 Plastid phylogenetic tree | Phylogenetic relationships were inferred from 53 species of the Apiaceae family by using Panax notoginseng (Arialaceae) as an outgroup. The 54 plastid genomes were retrieved from GenBank and aligned using MAFFT v7.450 under default parameters;… | 10.3390/ijms22189713 plastid alignment | MAFFT + Geneious Prime NJ | |||
| 10.3390/ijms22189713 rbcL phylogenetic tree | Phylogenetic relationships were inferred from 53 species of the Apiaceae family by using Panax notoginseng (Arialaceae) as an outgroup. rbcL sequences were extracted from plastid genomes retrieved from GenBank and aligned using MAFFT v7.450; the… | 10.3390/ijms22189713 rbcL alignment | MAFFT + Geneious Prime NJ | |||
| 2011 Carrot EST Assembly blast to DCARv2 | The assembled sequences from the 2011 Carrot EST Assembly were mapped to the carrot genome assembly DCARv2 using blastn. Resulting hits were converted to gff3 format for use in the CarrotOmics JBrowse. This file can be downloaded from the link… |
Additional file 2 | blastn | |||
| An Automated Image Analysis Pipeline Enables Genetic Studies of Shoot and Root Morphology in Carrot (Daucus carota L.) | L8708 × Z020 Linkage Map Variants The F2 population, L8708 × Z020, was identified from prior field screening as segregating for plant height, shoot biomass, and root storage shape and color. This population was derived from a cross… |
10.3389/fpls.2018.01703 | TASSEL | |||
| BGI Mobile Element Annotation | Mobile elements in the genome assembly were identified at both the DNA and protein level. RepeatMasker v3.2.9 (http://www.repeatmasker.org/) was applied to screen the genome assembly for low complexity… |
BGI | RepeatMasker | |||
| BGI Tandem Repeats Annotation | Tandem repeats were detected using Tandem Repeats Finder v4.07b. The annotation file used for JBrowse can be downloaded from the link below. Data from this analysis can be… |
BGI | Tandem Repeats Finder | |||
| Carrot Genome Assembly DCARv1 Gap Fill | This analysis represents one step of the whole genome assembly process, the gap fill process. This is described in section 1.3.1 of the Supplementary Note of the referenced publication. Gaps were filled using GapCloser for SOAPdenovo… |
BGI | GapCloser for SOAPdenovo | |||
| Carrot Genome Assembly DCARv2 Gaps | This analysis represents the JBrowse annotation of gaps in the assembled carrot genome sequence. This JBrowse track shows all gaps in the genome assembly consisting of runs of 1 or more 'N's. Gaps of exactly 1000nt are a special case, and… |
CarrotOmics 177698 | detection using regular expression | |||
| Carrot Genome Assembly DCARv3 Gaps | This analysis represents the JBrowse annotation of gaps in the assembled carrot genome sequence "Carrot Genome Assembly DH1 v3.0". This JBrowse track shows all gaps in the genome assembly consisting of runs of 100 'N's, which represent… |
Carrot Genome Assembly DH1 v3.0 | DCARv3 post-assembly annotation of gaps | |||
| Carrot Genome Assembly DH1 v3.0 Regulatory Gene Annotation | PlantTFcat, a reference plant transcription factor and transcriptional regulator categorization tool, was used to predict the transcription factors and regulatory genes in v3 gene models as well as the DCARv2 genes for comparison purposes. The… |
Carrot Genome Assembly DH1 v3.0 | PlantTFcat | |||
| Carrot Genome Assembly DH1 v3.0 Repetitive DNA Annotation | De novo identification of carrot repetitive DNA was carried out with RepeatModeler v.2.0.1. Annotation of the consensus sequences was performed using a curated database of carrot LTR-RTs, Helitrons and MITE, carrot… |
Carrot Genome Assembly DH1 v3.0 | RepeatModeler + RepeatMasker | |||
| Carrot Genome Assembly DH1 v3.0 Resistance Gene Annotation | PRGdb 3.0, a comprehensive platform for prediction and analysis of plant disease resistance genes, was used to predict the disease resistant genes in v3 as well as the v2 for the comparison purposes. The data from this analysis is presented in… |
Carrot Genome Assembly DH1 v3.0 | PRGdb | |||
| Carrot Genome Assembly DH1 v3.0 Tandem Repeats annotation by trf | Tandem repeat detection with Tandem Repeats Finder version 4.07b |
Carrot Genome Assembly DH1 v3.0 | Tanden Repeats Finder | |||
| Carrot Genome Assembly V.2 RNAseq population 70796 dOr vs. pOr | This analysis was part of the carrot genome assembly publication In population 97837, root tissue was collected from plants with yellow (yyY2Y2) and white (YYY… |
Population 70796 | Trimmomatic-TopHat-Cufflinks | |||
| Carrot Genome Assembly V.2 RNAseq population 97837 Y vs. W | This analysis was part of the carrot genome assembly publication In population 97837, root tissue was collected from plants with yellow (yyY2Y2) and white… |
Population 97837 | Trimmomatic-TopHat-Cufflinks | |||
| Cell Membrane Stability and Relative Cell Injury in Response to Heat Stress during Early and Late Seedling Stages of Diverse Carrot Germplasm | Leaf samples were collected for cell membrane stability estimation 30 days (Early Seedling (ES) developmental stage) or 52 days after planting (Late Seedling (LS) developmental stage). Cell membrane stability of heat-treated and… |
10.21273/HORTSCI15058-20 | 10.21273/HORTSCI15058-20 | |||
| Daucus carota genome V.3 SSR Detection with MISA | SSRs were detected in the Daucus carota V.3 assembly using misa, and when possible primers were designed with primer3. misa detection parameters 2-6 3-4 4-3 5-3 6-3 7-3 8-3 and interruptions 10 This analysis has not been published… |
Carrot Genome Assembly DH1 v3.0 | misa + primer3 | |||
| DCAR Gene annotation V1.0 locations on Carrot Genome Assembly DH1 V3.0 | Gene predictions from the Carrot Genome Assembly DCARv2 were transferred to the Carrot Genome Assembly DCARv3 using GMAP. Organellar annotations were transferred separately using CrossMap with manual corrections for trans-spliced genes. |
Carrot Genome Assembly DH1 v3.0 | GMAP and CrossMap | |||
| DCAR peptide blastp to SwissProt and TrEMBL without DCAR | This analysis is a blastp search of all of the DCAR V1.0 Gene Prediction polypeptide sequences against combined ExPASy SwissProt and TrEMBL databases from Nov. 17, 2021. Prior to performing the blast search, the… |
DCAR_ExPASy_20211117 | blastp | blastp to SwissProt and TrEMBL without DCAR | ||
| DCARv2 Mapped Markers | This meta analysis collects all markers from all linkage maps that have a known genome location in the DCARv2 carrot genome assembly. This information is available in the JBrowse track "Mapped Markers" |
CarrotOmics 291908 | Data from CarrotOmics | |||
| Genome Paper Variants 2016 | We used BWA-MEM version 0.7.10 to map the resequencing reads from all carrot genotypes to the carrot reference genome using the following parameters -a -M –t 42. Alignments were filtered using SAMtools version 0.1.19 for only primary alignments… |
CarrotOmics 177695 | bwa; SAMtools; Picard; the GATK | |||
| Germplasm Image Acquisition for SCRI Project - 2018 | Images from carrot roots grown in 2018 used by the SCRI Project Grown at the University of Wisconsin Hancock Agricultural Research Station (44.117850, -89.552265) from May to October 2018. |
SCRI 2022 | Photography |