How does the IMAGE pipeline for production of cDNA clones work?
The IMAGE consortium puts clones into the catagories of EST, Putative Full-Length and Full-Length. This is because there is a pipeline that the clones go through to be analyzed to see if they are full-length or not. A cDNA library is made and the clones are arrayed out into individual wells in a microtiter plate. At this point a clone will be labeled as EST or Putative Full-length depending on the library that it came from. All of the clones are end-sequenced on the 5' end of the clone. They do this end read to analyze the clones looking for a start codon. This sequence is posted to GenBank associated with the clone ID. If a start codon is found, the clone is then fully sequenced and the SAME clone is re-arrayed onto a NEW PLATE (if it is an EST) where it is labeled PUTATIVE FULL-LENGTH. (This sequence is also posted to GenBank associated with the clone ID. You can tell that a sequence posted to GenBank is a full insert read, because the accession number of a full insert read STARTS WITH "BC". ) If the clone was already on a putative-full length plate, then it does not move at this point. Putative full-length seems to be the most misunderstood of all the labels. All that Putative Full-length means is that the IMAGE consortium thinks that it might be full-length. Whether or not it is found to be full-length later, the clone in that particular plate will ALWAYS be known as Putative full-length. After full-insert sequencing, the sequence of the clone is analyzed and must pass 8 or 9 criteria put forth by the IMAGE consortium in order to be called "Full-length". If the clone passes all criteria, it is moved to a NEW PLATE and labeled as FULL-LENGTH. THIS IS A LABEL PUT ON THE CLONE BY IMAGE, WE HAVE NOTHING TO DO WITH THESE LABELS. EVEN IF IMAGE CALLS A CLONE FULL-LENGTH, THE RESEARCHER NEEDS TO LOOK AT THE "BC" SEQUENCE TO MAKE SURE THE CLONE MEETS THEIR EXPECTATIONS FOR A FULL-LENGTH CLONE. Plate location group labels (EST, Putative Full-length, or Full-length) are permanantly associated with each clone based on the plate location. So one particular clone can be found labeled as all 3 - EST, Putative-full Length, and Full-length. It is still the SAME clone in all 3 types of microtiter plates, it has just made it's way through the pipeline.