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       Access to individual ESTs and assemblies

    CGP database provides access to individual libraries constructed by CGP group as well as to assemblies of all available ESTs at NCBI GenBank. Assemblies of all available ESTs may contain sequences from libraries generated by other research groups.


       Library Info

    Web pages under links 'Access to CGP library' display assembly info per individual library generated by CGP group. In library info dataset all ESTs have original IDs as they were provided by sequencing facilities (like QGA11P20.yg.ab1 or CLLZ3791.b2_N12.ab1). Access to all CGP libraries on one web page is available at http://cgpdb.ucdavis.edu/cgpdb2/est_info_library.php

    Data files available for download and analysis:

  • ESTs_FILE file in FASTA format with individual ESTs per particular library
  • ASSEMBLY_FILE file in FASTA format with assembled ESTs (unigene set) for particular library
  • CLUSTER_INFO file with information about contig complexity (list of ESTs per contig)
  • ATH_BLAST_INFO BLAST search of unigene set (assembly) versus Arabidopsis protein sequences; first best hit only


       Assembly Info

    Web pages under links 'Access to CGP Assembly Information' display assembly info per species for all available ESTs at NCBI GenBank. These assemblies include ESTs from CGP and other research groups if available. In each assembly dataset all ESTs have GenBank accession IDs with species specific nine-letter prefix (for example, Lact_sati.BQ876105 or Heli_annu.BU036492). Access to all Compositae assemblies on one web page is available at http://cgpdb.ucdavis.edu/asteraceae_assembly/

    Data files available for download and analysis:

  • SEQs_FILE file with individual ESTs in FASTA format
  • ASSEMBLY_FILE CAP3 assembly of individual ESTs (unigene set)
  • CONTIG_INFO contig complexity info (how many ESTs per contig and their ID list)
  • CAP3_ALIGNMENTS tar.gz file with individual EST alignments per contig to use and view it with Python Contig Viewer http://cgpdb.ucdavis.edu/asteraceae_assembly/ContigViewer/
  • ATH_BLAST_INFO_BEST_HIT results of BLAST search assembly versus Arabidopsis proteins; first best hit only


       Asteraceae (Compositae) Resources at NCBI (PowerPoint presentation)
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