Currently database contains the following tables:

• Lettuce_Contigs_ID, Sunflower_Contigs_ID - list of contigs produced by CAP3 assembly. Tables contain information which ESTs were used to assemble particular contig and size of fragment overlaps. By clicking on Contig_ID you can view actual sequence alignment.
  
  
• Lettuce_Info, Sunflower_Info - tables contain information about TAGs for each EST read. If an EST read belongs to a contig, this information is given in a column "Cluster_ID". Column "Seqs_N" shows how many other EST reads belong to a given contig. By clicking on "EST_ID" you can view the actual chromatogram. Note, that chromatogram viewer displays untrimmed unmasked raw reads. Chromatogram viewer is written in Java and works with Netscape-7 and IE-6.
  
  
• lettuce_all_reads_trimmed, sunflower_all_reads_trimmed - Actual set of sequences after trimming, visual inspection and additional semi-manual trimming which were used for contig assembly. By clicking on "Sequence_ID" you can view the actual chromatogram.
  
  
• lettuce_assembly, sunflower_assembly - CAP3 assembly of trimmed sequences. Tables contain information about all contigs and singletons (unigene set). In other words, there are a non-redundant datasets.
  
  
• lettuce_assembly_blastX, sunflower_assembly_blastX - Results of blastX search against nr protein database at NCBI of unigene set. 24 best hits (if found) represented for each contig or singleton. Normalized expectation is: (-log(exp))/100
  
  
• lettuce_vs_ath_TIGR, sunflower_vs_ath_TIGR - Results of blastx search against Arabidopsis TIGR database (predicted ORFs) of unigene set. 48 best hits (if found) represented for each contig or singleton. Normalized expectation is: (-log(exp))/100
  
  
• lettuce_pfam, sunflower_pfam - results of hmmrsearch for Pfam domains in the translated regions of the assemblies.
  
  
• lettuce_clustering, sunflower_clustering - Results of tblastx search EST assembly against itself. Two sequences considered as linked if they have identity at least 40% with sequence overlap at least 100 amino acids (based on blast translation). Clustering was done using tcl_blast_parser_123_V007.tcl and Graph9 programs. Example of clustering visualization you can find here.
  
  

Contig Viewer navigation:

Meaning of EST designation

Contigs:
QG_CA_Contig#### or QH_CA_Contig#### - "QG" stands for Lettuce dataset, "QH" stands for Sunflower dataset.

Lettuce EST reads:
QGA QGB QGC QGD QGI = QG_(A,B,C,D,I) libraries - cultivated lettuce, Salinas (multiple tissues and growth conditions identified by TAG IDs)

QGE QGF QGG QGH QGJ = QG_(E,F,G,H,J) libraries - wild lettuce, Lactuca serriola (multiple tissues and growth conditions identified by TAG IDs)


Sunflower EST reads:
QHA QHB QHC QHD QHI = QH_(A,B,C,D,I) libraries - sunflower RHA801 (multiple tissues and growth conditions identified by TAG IDs)

QHE QHF QHG QHH QHJ = QH_(E,F,G,H,J) libraries - sunflower RHA280 (multiple tissues and growth conditions identified by TAG IDs)

QHK QHL - Helianthus paradoxus (seedling, root, leaf and flower tissues) (no TAG IDs are available)
QHK - normal growth conditions
QHL - salt stress

QHM QHN - Helianthus argophyllus (seedlings, root and leaf tissues) (no TAG IDs are available)
QHM - normal growth conditions
QHN - drought stress


TAG IDs description:

Lettuce:
TAG0 - callus
TAG1 - roots
TAG2 - none
TAG3 - flowers pre-fertilized
TAG4 - flowers post-fertilized
TAG5 - chemical induction
TAG6 - none
TAG7 - roots environmental stress
TAG8 - shoots environmental stress
TAG9 - germinating seeds
TAG10 - flowers environmental stress
TAG11 - leaves dark grow


Sunflower:
TAG0 - callus
TAG1 - roots
TAG2 - disk and ray flowers
TAG3 - flowers pre-fertilized
TAG4 - developing kernel
TAG5 - chemical induction
TAG6 - none
TAG7 - roots environmental stress
TAG8 - shoots environmental stress
TAG9 - germinating seeds
TAG10 - flowers environmental stress
TAG11 - hulls