############################################################ # Construction of the grape goldenpath # and naming convention of chromosomes # 12/02/2010 - vitis AT genoscope.cns.fr ############################################################ Random chromosomes contains sequences that have been assigned to grape chromosome but we could not determine their position on this chromosome relative to other sequences. They are thus placed as individual fasta files in an arbitrary (random) order in chromosomeN_random. The sequence in "chromosomeN" is a set of ultracontigs and supercontigs that have all been placed relative to each other. ChrUn_random contains ultracontigs that can't be placed on a specific chromosome. We essentially just concatenate together all these ultracontigs into one artificial chromosome. The coordinates of these are fairly arbitrary, although within an ultracontig the relative positions of the coordinates are good. Between two ultracontigs in the chrUn_random artificial chromosome, we add a stretch of 500 N's. The file chr.agp has a set of lines starting with chrN_random which either defines a chunck of sequence or a gap, in the order they come in the chromosomeN_random file. The definition of each type is to be found in the file chr.agp.info in that directory.