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Welcome to the Dendrome Project!

 Resources

Scripts BLAST FASTA Readseq Galaxy Tools Databases TreeGenes Plant Ontology iPlant Downloads

 Links

Conifer Genome Network PineRefSeq Project SMarTForests Project Conifer Translational Genomics Network TreeGenes Database Dendrome Plone Forestry Careers and Education Resource

 Contact

tg-help@ucdavis.edu

Blast Databases

General Nucleotide Blast Databases

Database Description Links Last Updated chloroplast.fna Chloroplast Genome Sequence from select species [More_Info] 05/13/2013 est_others Sequence data and other information on single-pass cDNA sequences from NCBI [More_Info] 04/05/2013 mito.nt Mitochondrial Nucleotide from Plants [More_Info] 05/10/2013 nt NCBI Nucleotide Retrieval [More_Info] 05/10/2013 plant.genomic Combined Plant genomic from NCBI [More_Info] 05/10/2013 plant.rna Combined Plant RNA from NCBI [More_Info] 05/10/2013 plant.unigene Combined Plant Species Unigene set from NCBI [More_Info] 04/05/2013 refseq_genomic Refseq Genomic from NCBI [More_Info] 04/05/2013 refseq_rna Refseq RNA from NCBI [More_Info] 05/10/2013

Species-Specific Nucleotide Blast Databases

Database Description Links Last Updated AllSpeciesAmplicons.nt Sanger resequenced amplicons in # conifers from EST contigs [More_Info] 01/13/2012 At.seq.uniq Unigene set for Arabidopsis thaliana from NCBI [More_Info] 01/07/2013 Mtr.seq.uniq Unigene set for Medicago truncatula from NCBI [More_Info] 04/05/2013 Nta.seq.uniq Unigene set for Nicotiana tabacum from NCBI [More_Info] 01/07/2013 Os.seq.uniq Unigene set for Oryza sativa from NCBI [More_Info] 01/07/2013 Pgl.seq.uniq Unigene set for Picea glauca from NCBI [More_Info] 01/07/2013 pila_transcriptomev1.nt TreeGenes Transcriptome Assembly v1.0 for Pinus lambertiana 01/13/2012 PitaSangerAmplicons.nt Sanger resequenced amplicons from EST contigs in Pinus taeda [More_Info] 01/13/2012 pita_transcriptomev1.nt TreeGenes Transcriptome Assembly v1.0 for Pinus taeda [More_Info] 01/13/2012 Ppa.seq.uniq Unigene set for Physcomitrella patens from NCBI [More_Info] 01/07/2013 Ppe.seq.uniq Unigene set for Prunus persica from NCBI [More_Info] 01/07/2013 Psi.seq.uniq Unigene set for Picea sitchensis from NCBI [More_Info] 01/07/2013 psme_transcriptomev1.nt TreeGenes Transcriptome Assembly v1.0 for Pseudotsuga menziesii [More_Info] 01/13/2012 ptaeda.v0.6.contigs Pinus Taeda Genomic Assembly Contigs V0.6 [More_Info] 07/05/2012 ptaeda.v0.6.scaffolds Pinus Taeda Genomic Assembly Scaffolds V0.6 [More_Info] 07/05/2012 Pta.seq.uniq Unigene set for Pinus taeda from NCBI [More_Info] 01/07/2013 Pth.seq.uniq Unigene set for Populus trichocarpa from NCBI [More_Info] 01/07/2013 Ptp.seq.uniq Unigene set for Populus tremula X Populus tremuloides from NCBI [More_Info] 01/07/2013 Qro.seq.uniq Unigene set for Quercus robur from NCBI [More_Info] 01/08/2013 Sbi.seq.uniq Unigene set for Sorghum bicolor from NCBI [More_Info] 01/08/2013 tair.cds TAIR10 CDS from Arabidopsis [More_Info] 01/07/2013 tair.seq TAIR10 Nucleotide from Arabidopsis [More_Info] 01/07/2013 Vvi.seq.uniq Unigene set for Vitis vinifera from NCBI [More_Info] 04/05/2013 Zm.seq.uniq Unigene set for Zea mays from NCBI [More_Info] 01/08/2013

Protein Blast Databases

Database Description Links Last Updated chloroplast.faa Chloroplast Proteins from select species [More_Info] 05/13/2013 mito.aa Mitochondrial Protein from Plants [More_Info] 05/10/2013 nr NCBI non-redundant Proteins [More_Info] 04/05/2013 plant.protein Combined Plant Proteins from NCBI [More_Info] 05/10/2013 refseq_protein Refseq Protein from NCBI [More_Info] 05/10/2013 swissprot Swissprot annotated protein sequence from NCBI [More_Info] 05/10/2013 tair.pep TAIR10 Proteins from Arabidopsis [More_Info] 01/07/2013

 Updates

PineRefSeq project releases assembly (v0.9) of the Pinus teada genome CartograTree (v2.0.0) , a map interface that works with DiversiTree to bring together genomics, ecological, and trait data is now live! SMarTForests Project releases the first assembly (v1.0) of the Picea glauca genome

 Events

Galaxy Community Conference

Oslo, Norway
June 30-July 2, 2013 2013 Symposium of the American Genetic Association

Cornell University, Ithaca, NY USA
July 20-22, 2013 Forest Genetics 2013 - Canadian Forest Genetics Assoc; WFGA; IUFRO Population, Ecological & Conservation Genetics; IUFRO Breeding PNW Conifers

Hilton Hotel, Whistler, BC, Canada
July 22-25, 2013