Welcome to CGP2

Data Access

EST Library Info

Library Construction Info

EST Assembly Info (CGP1 and CGP2 projects)

Assemblies of all Compositae sequences available at NCBI EST database

CGP_ContigViewer

BLAST search against EST assemblies (Not available)

Search BLASTX table by keyword (Not available)

Sequence retrieval by ID from database (Not available)

Python and Tcl/Tk scripts and tools to process and analyze DNA sequences and related data

Compositae Resources at NCBI



CGP1 - access to old CGPDB project data (2000 - 2004)



List of publications where Compositae DB has been used as a primary source of data



EST Library Analysis Reference Files:

ANALYSIS OF EST LIBRARIES WAS PERFORMED WITH THE FOLLOWING REFERENCE GENOME SETS:

NCBI Plant RefSeq SET
PlantRefSeq_2006_10_03_SP.fasta

ARABIDOPSIS GENOME REFERENCE SET:
A_thaliana_ATGC_2006_08_24.cds_dna.fasta - predicted open reading frames, DNA file
A_thaliana_ATGC_2006_08_24.protein.fasta - predicted open reading frames, translated 'protein' file
A_thaliana_ATGC_2006_08_24.xcoords.tab - genome coordinates of predicted ORFs

SINGLE COPY ARABIDOPSIS GENES:

A_thaliana_ATGC_2006_08_24.cds_dna.COS_STRICT.fasta - single copy genes (DNA), 3790 plant (Arabidopsis) specific sequences
A_thaliana_ATGC_2006_08_24.protein.COS_STRICT.fasta - single copy genes (proteins), 3790 plant (Arabidopsis) specific sequences
A_thaliana_ATGC_2006_08_24.protein.COS_STRICT.IDs.txt - single copy genes, 3790 plant (Arabidopsis) specific sequence IDs

A_thaliana_ATGC_2006_08_24.cds_dna.COS_ULTRA.fasta - single copy genes (DNA), 357 eukaryotic specific sequences
A_thaliana_ATGC_2006_08_24.protein.COS_ULTRA.fasta - single copy genes (proteins), 357 eukaryotic specific sequences
A_thaliana_ATGC_2006_08_24.protein.COS_ULTRA.IDs.txt - single copy genes, 357 eukaryotic specific sequence IDs

C.elegans:
C_elegans_ATGC_2006_08_24.protein.COS_ULTRA.fasta - single copy genes (proteins), 356 eukaryotic specific sequences


EST analysis, UCO (ultra conserved orthologs) stat




View some SNPs/InDels from Lettuce CDS assembly




Lettuce Genetic Map Viewer

current version of the genetic map Salinas X Serriola RILs

Genetic Map Raw Data

CGPDB Excel Data Submission Templates

MadMapper