I am interesting in Ests and which ones get selected for the database for the browser. How do you update Text-Based Table Browser?
Response: First, the new assembly has to be completed using newly finished contigs. That fills many gaps, correctly orients many strands, reduces artefactual duplications necessary in the optimal compromise assembly, and improves coordinate numbering of almost every nucleotide in the genome, relative to the previous build. Second, each track and its corresponding table have to be aligned on the new assembly to find their new coordinates. Of course, there may be many brand new est sequences too. These would not have coordinates at all in the previous build. The tables have various fields as described individually but the key concepts (say for a spliced est) are its start and stop coordinates of each blocks that match in the genome. Only when a table is complete, and some of these are very computationally intensive, can its track can appear in the browser. All human ests in GenBank on the date of the freeze are used. Even if two happened to have the identical sequence, both would be reta
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