This track shows the draft assembly of the platypus genome.
Combined whole genome shotgun plasmid, fosmid and BAC end sequence reads
were assembled using the PCAP software (Huang, et al.,
2003) using stringent parameters. After initial assembly with the PCAP
software, "supercontigs" (ordered/oriented contigs; contigs are
contiguous sequences not interrupted by gaps) were linked to the
physical map (Washington University Genome Sequencing Center) using
BAC end sequences and in silico digests of the sequence itself. The
physical map, then, was used to organize the supercontigs into
"ultracontigs" (ordered/oriented supercontigs). With the exception of
those supercontigs with alignments at >95% identity to a platypus
EST (Washington University Genome Sequencing Center), supercontigs smaller
than 2 kb were removed from the data set prior to submission if they
were >97% identical over >97% of their length to other ultracontigs
larger than 2 kb or if they were deemed to be >95% repetitive (based on
analysis using RECON (Bao and Eddy, 2002) for repeat
identification). Further, singleton contigs (those not part of a
supercontig or ultracontig) smaller than 500 bp that did not have
an alignment of >95% identity to a platypus EST were not submitted.
In dense mode, this track depicts the contigs that make up the
currently viewed chromosome or ultracontig.
Contig boundaries are distinguished by the use of alternating gold and brown
coloration. Where gaps
exist between contigs, spaces are shown between the gold and brown
blocks. The relative order and orientation of the contigs
within an ultracontig is always known; therefore, a line is drawn in the graphical
display to bridge the blocks.
All components within this track are of fragment type "W":
Whole Genome Shotgun contig.