Cacao Matina1-6 Genome v1.1

Details
Analysis Name Cacao Matina1-6 Genome v1.1
Software Customized version of the Arachne2 assembler (in-house) (in-house)
Source Roche 454 Titanium STD reads (USDA-ARS, Stoneville)
Date performed 2012-03-28
Description

Theobroma cacao Matina1-6 v1.1 Release

From this page you can read about the genome sequence assembly statistics and annotation protocol, browse and download the whole v1.1 genome sequence; predicted gene transcripts, their locations and putative function based on homology to known genes in Arabidopsis and SwissProt. You can BLAST your sequences against the genome sequence, and the predicted gene transcripts and peptides. You can search and browse the chromosomes, contigs, markers, and genes in GBrowse and view the evidence for each prediction and feature.
 

Genome v1.1 Statistics

The resulting pseudomolecules (numbered 1-10) capture 94.6% of the  assembled sequence and 98.2% of the sample EST set.

 

More Information

 

Organisms Theobroma cacao
Downloads

Cacao Genome Sequence (v1.1)
Scaffolds (FASTA file, 97MB compressed) Cacao_genome_v1.1_Scaffolds.fa.gz
Scaffolds  w/ masked repeats (FASTA file, 101MB compressed) Cacao_genome_v1.1_Scaffolds_RM.fa.gz
Scaffolds  (GFF3 file, 55KB) Cacao_genome_v1.1_Scaffolds.gff3


 Cacao Genome Genome Annotation (v1.1)
Predicted gene transcripts (FASTA file, 28MB compressed) Cacao_genome_v1.1_transcript.fa.gz
Predicted gene peptides (FASTA file, 11MB compressed) Cacao_genome_v1.1_peptide.fa.gz
Predicted gene CDs (FASTA file, 17MB compressed) Cacao_genome_v1.1_cds.gz


Cacao predicted genes blastp vs protein databases. Best hit reports in Excel
UniProtKB/Swiss-Prot (5.3MB) Cacao_genome_v1.1_vs_sprot.xlsx
UniProtKB/TrEMBL (38.2MB) Cacao_genome_v1.1_vs_TrEMBL.xls
TAIR10 (arabidopsis) proteins (4.8MB) Cacao_genome_v1.1_vs_arabidopsis.xlsx
Prunus persica (peach) v1.0 proteins (4.5MB) Cacao_genome_v1.1_vs_peach.xlsx
Vitis vinifera (grape) proteins (4.3MB) Cacao_genome_v1.1_vs_grape.xlsx
Populus trichocarpa (poplar) v2.0 proteins (4.6MB) Cacao_genome_v1.1_vs_poplar.xlsx