Whats the easiest way for users to find the TRUE ends, and thus the insert size, of a clone?
The set of clone ends is dumped as part of the gff files: http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/GFF_files.shtml This is the source for the extents displayed in WormBase. The caveat with this is that the ‘true’ end is not marked up for all clones. The early cosmids do not have such annotations because nobody thought about marking them up. Later cosmids do have clone left and right ends as this became part of the standard procedure. Finally, many of the YACs do not have clone ends because the segment submitted to GenBank/EMBL is much smaller than the full clone, and hence the true ends lie within sequences already finished at that stage of the sequencing (i.e. we never went back to update clone ends in sequence already finished).
