DCARv2 V1.0 Gene Prediction JBrowse GFF3

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File
File Type: 
GFF3
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Download File NameAvailable atSizeMD5
22.dcar-for-jbrowse.gff3.gzCarrotOmics26.58MB38f6bd9790688c1cf1cb4880dcd0522a
Description: 

Gene prediction V1.0 for the DCARv2 genome assembly. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

References: 
The following records refer to this file:
Genome AnnotationLoading content
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Analysis: 
NameDescription

For gene model prediction, mobile element–related repeats were masked using RepeatMasker. De novo prediction using AUGUSTUS v2.5.5, GENSCAN v.1.1.0, and GlimmerHMM-3.0.1 was trained using model species A. thaliana and S. lycoperisum training sets. The protein sequences of S. lycoperisum, Solanum tuberosum, A. thaliana, Brassica rapa, and Oryza sativa were mapped to the carrot genome using TBLASTN (BLAST All 2.2.23) and analyzed with GeneWise version 2.2.0. Carrot ESTs were aligned to the genome using BLAT and analyzed with PASA to detect spliced gene models. RNA-seq reads from 20 DH1 libraries were aligned with TopHat 2.0.9. Transcripts were predicted by Cufflinks. All gene models produced by de novo prediction, protein homology searches, and prediction and transcript-based evidence were integrated using GLEAN v1.1. Putative gene functions were assigned using the best BLASTP match to SwissProt and TrEMBL databases. Gene motifs and domains were determined with InterProScan version 4.7 against the ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE protein databases. GO IDs for each gene were obtained from the corresponding InterPro entries. All genes were aligned against KEGG (release 58) proteins.

Data from this analysis can be viewed in JBrowse here.

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Organism: 
NameCommon NameComment
Carrot
For a general overview of carrot, see the Carrot Facts Page
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License: 
NameAttribution 4.0 International (CC BY 4.0)
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